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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
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===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in ''Streptomyces coelicolor'' genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of ''nar'' genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the ''nar'' genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of ''Streptomyces coelicolor''. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capable of metabolizing other organism's remains. They are especially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
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==Pathology==<br />
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''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
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''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very important to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmaceutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosuppressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the developmental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterization of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the ''Streptomyces'' Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “''Streptomyces Coelicolor'' A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “''Streptomyces'': Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of ''Streptomyces Coelicolor'' A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in ''Streptomyces''". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of ''Streptomyces coelicolor'': Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in ''Streptomyces coelicolor'' Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15236Streptomyces coelicolor2007-06-05T02:20:22Z<p>Afritch: /* Current Research */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
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===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
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<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in ''Streptomyces coelicolor'' genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of ''nar'' genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the ''nar'' genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of ''Streptomyces coelicolor''. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capable of metabolizing other organism's remains. They are especially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very important to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmaceutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosuppressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the developmental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterization of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15226Streptomyces coelicolor2007-06-05T02:17:04Z<p>Afritch: /* Application to Biotechnology */</p>
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<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in ''Streptomyces coelicolor'' genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of ''nar'' genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the ''nar'' genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of ''Streptomyces coelicolor''. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capable of metabolizing other organism's remains. They are especially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very important to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmaceutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosuppressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
<br />
The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15219Streptomyces coelicolor2007-06-05T02:15:40Z<p>Afritch: /* Ecology */</p>
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<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in ''Streptomyces coelicolor'' genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of ''nar'' genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the ''nar'' genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of ''Streptomyces coelicolor''. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capable of metabolizing other organism's remains. They are especially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
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''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15203Streptomyces coelicolor2007-06-05T02:08:56Z<p>Afritch: /* Cell structure and metabolism */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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{|<br />
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'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in ''Streptomyces coelicolor'' genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of ''nar'' genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the ''nar'' genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of ''Streptomyces coelicolor''. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15196Streptomyces coelicolor2007-06-05T02:04:52Z<p>Afritch: /* Description and significance */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is available about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The ''Streptomyces'' genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15056Streptomyces coelicolor2007-06-05T01:31:59Z<p>Afritch: /* Ecology */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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{|<br />
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|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is availabe about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(3). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=15055Streptomyces coelicolor2007-06-05T01:31:29Z<p>Afritch: /* Ecology */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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{|<br />
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|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is availabe about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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As mentioned earlier, the ''Streptomyces'' genus produces many different types of antibiotics. Since ''Streptomyces coelicolor'' cannot "move", antibiotic production provides a useful way to eliminate competition for nutrients in the soil(4). ''Streptomyces'' species are abundant in the soil, so this ability definitely has an effect on whether other soil bacteria will be able to live near them.<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
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''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
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(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=14884Streptomyces coelicolor2007-06-05T00:41:21Z<p>Afritch: /* Current Research */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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{|<br />
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|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is availabe about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
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(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
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(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=14880Streptomyces coelicolor2007-06-05T00:39:50Z<p>Afritch: /* References */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
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'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is availabe about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
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''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
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''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
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(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
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(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
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(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
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(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
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(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
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(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
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(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
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(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
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(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
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(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
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(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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(25) Hopwood, David A. "Forty Years of Genetics with ''Streptomyces'': from ''in vivo'' through ''in vitro'' to ''in silico''." (1999) <u>Microbiology</u> 145. p. 2183-2202. [http://mic.sgmjournals.org/cgi/reprint/145/9/2183?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Hopwood&title=Streptomyces&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Link to Aritcle]<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=14872Streptomyces coelicolor2007-06-05T00:35:44Z<p>Afritch: /* Description and significance */</p>
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<div>{{Biorealm Genus}}<br />
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==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
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{|<br />
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|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, aerial mycelium lacking spirals, and no melanoid pigment(5). Since the A3(2) strain is actually ''Streptomyces violaceoruber'', it looks a bit different. One distinction is that the A3(2) strain has ash gray aerial mycelium with spirals(5). From this point on, I will refer to ''Streptomyces coelicolor'' as the A3(2) strain and not Muller's strain because the A3(2) strain was sequenced, and a great deal of information is availabe about it. ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
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==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
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==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
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''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
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==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
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The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
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The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
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==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
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(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
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(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
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(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
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(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
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(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
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(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
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(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
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(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
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(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=14807Streptomyces coelicolor2007-06-05T00:14:44Z<p>Afritch: /* Description and significance */</p>
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<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber'' genus, although it retains the former name, and is not the same strain as the Muller strain(25). ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions. Other differentiating characteristics of Muller's ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
<br />
The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=14799Streptomyces coelicolor2007-06-05T00:12:46Z<p>Afritch: /* Description and significance */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. The ''Streptomyces coelicolor'' <br />
A3(2) strain studied in depth by David A Hopwood and sequenced by the John Innes Center and the Sanger Institute is actually taxonomically a member of the ''Streptomyces violaceoruber<br />
'' genus, although it retains the former name, and is not the same strain as the Muller strain. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
<br />
The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12944Streptomyces coelicolor2007-06-03T07:27:39Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
<br />
The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828. [http://www.genome.org/cgi/reprint/15/6/820 Link to Article]<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 2.1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. [http://jb.asm.org/cgi/reprint/189/6/2219?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=189&issue=6&resourcetype=HWCIT Link to Article] <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17427251 Link to Abstract]<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192. [http://jb.asm.org/cgi/content/full/183/10/3184?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=streptomyces+coelicolor&searchid=1&FIRSTINDEX=0&volume=183&issue=10&resourcetype=HWCIT Link to Article]<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. [http://www.biochemsoctrans.org/bst/033/0210/0330210.pdf Link to Article] <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. [http://aem.asm.org/cgi/content/full/69/4/2201?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=Sweet+Potato&searchid=1&FIRSTINDEX=0&volume=69&issue=4&resourcetype=HWCIT Link to Article]<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
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<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12919Streptomyces coelicolor2007-06-03T07:02:33Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
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Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
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'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
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==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20).<br />
<br />
The ''bld'' genes are responsible for differentiation in ''Streptomyces coelicolor''. Researchers have determined how the protein BldD interacts in the cell to accomplish this purpose. BldD is a homodimeric, DNA binding protein that has two separately folding subunits. The N terminal half of the protein was determined to be responsible for dimerization and DNA binding. The structure and function of this protein show that BldD may have a very great influence in the develpomental stages of ''Streptomyces coelicolor''(14). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. <br />
<br />
(14) Lee, C.J., H.S. Won, J.M. Kim, B.J. Lee, and SO Kang. "Molecular <br />
Domain Organization of BldD, an Essential Transcriptional Regulator for Developmental Processes of ''Streptomyces coelicolor'' A3(2)." <u>Proteins</u>. 68.1 p. 344-352.<br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12911Streptomyces coelicolor2007-06-03T06:46:27Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
Research is currently being done to discover the function of different genes in ''Streptomyces coelicolor'' since its complete genome has now been sequenced.<br />
<br />
Recent research has determined that a group of ''mtbH''-like genes is ''Streptomyces coelicolor'' are necessary for some secondary metabolite production. ''Streptomyces coelicolor'' has three such genes, one of which is ''cloY''. When all three genes were absent, clorobiocin, an antibiotic, was produced only in very small amounts, but when ''cloY'' was restored, clorobiocin was produced at a more significant level. This research also shows that the three genes may be able to "functionally replace each other"(20). <br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12801Streptomyces coelicolor2007-06-03T03:31:16Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato(2). Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(5). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria(4). The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation(3). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions(7). The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number(8). <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells(11). The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet(16). Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants(15).<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching mycelium network. Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it(13). Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air(12). The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration(13).<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade(19). This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''(20). <br />
Undecylprodigiosin, also known as Red, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes(21). Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms(23). Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives(22).<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006(10).<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225. <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12796Streptomyces coelicolor2007-06-03T03:16:23Z<p>Afritch: /* Pathology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes(17,18).<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12774Streptomyces coelicolor2007-06-03T02:38:08Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12772Streptomyces coelicolor2007-06-03T02:36:58Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI:[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock ]<br />
'''<br />
|}(1)<br />
<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12771Streptomyces coelicolor2007-06-03T02:34:34Z<p>Afritch: /* Genus */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1902&lvl=3&lin=f&keep=1&srchmode=1&unlock<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12764Streptomyces coelicolor2007-06-03T02:23:17Z<p>Afritch: /* Classification */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]<br />
'''<br />
|}(1)<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12706Streptomyces coelicolor2007-06-03T01:33:12Z<p>Afritch: /* Classification */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12687Streptomyces coelicolor2007-06-03T01:19:24Z<p>Afritch: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade. This ability makes them an integral part of the global carbon cycle.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12651Streptomyces coelicolor2007-06-03T00:45:02Z<p>Afritch: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.(24)<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12648Streptomyces coelicolor2007-06-03T00:44:15Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
(24) "Species Specific Metabolic Pathways: ''Streptomyces ceolicolor''." <u>Systems Biology Model Repository</u>. 1 Jun 2007. [http://www.systems-biology.org/001/001.html Link to Website] ''The metabolic pathways listed on this website were taken from the Kyoto Encyclopedia on Genes and Genomes as part of the JST ERATO-SORST Kitano Symbiotic Systems Project.''<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12638Streptomyces coelicolor2007-06-03T00:36:02Z<p>Afritch: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
''Streptomyces coelicolor'' also takes part in the nitrogen cycle. Several ''nar'' genes, as well as a few others, code for the products necessary to reduce nitrate to nitrite. Nitrite is reduced to ammonia by products coded for in ''nir'' genes as well. The role of decomposers, like ''Streptomyces coelicolor'', as nitrogen reducers is a major step in the nitrogen cycle.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12602Streptomyces coelicolor2007-06-03T00:11:49Z<p>Afritch: /* Cell structure and metabolism */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is an obligate aerobe. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12011Streptomyces coelicolor2007-05-31T05:30:49Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12010Streptomyces coelicolor2007-05-31T05:29:34Z<p>Afritch: /* Pathology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12009Streptomyces coelicolor2007-05-31T05:28:37Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]]<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditionsOther differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]]<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12008Streptomyces coelicolor2007-05-31T05:20:21Z<p>Afritch: /* Application to Biotechnology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]] Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]] <br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Streptomyces_jewels.jpg|thumb|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]]<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis'' <br />
Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12006Streptomyces coelicolor2007-05-31T05:17:36Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]] Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
[[Image:Blue_Streptomyces.jpg|thumb|"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC]]] <br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''.[[Image:Streptomyces_jewels.jpg|thumg|"Jewels in the crown of a Streptomyces colony are antibiotic secretions" (3) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
]] Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12005Streptomyces coelicolor2007-05-31T05:12:54Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg|thumb|''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] ]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''. Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12004Streptomyces coelicolor2007-05-31T05:07:03Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''. Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
(22) Demain, Arnold L. "Contribution of Genetics to the Production and Discovery of Microbial Pharmaceuticals." (1988) <u>Pure and Applied Chemistry</u>. 60.6 p. 833-836. [http://www.iupac.org/publications/pac/1988/pdf/6006x0833.pdf Link to Article] <br />
<br />
(23) Ichinose, Koji, Takaaki Taguchi, David J. Bedford, Yutaka Ebizuka, and David A. Hopwood. "Functional Complementation of Pyran Ring Formation in Actinorhodin Biosynthesis in ''Streptomyces coelicolor'' A3(2) by Ketoreductase Genes for Granaticin Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 p. 3247-3250. [http://jb.asm.org/cgi/reprint/183/10/3247.pdf Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12003Streptomyces coelicolor2007-05-31T05:05:26Z<p>Afritch: /* Application to Biotechnology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''. Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes. Actinorhodin is another antibiotic produced by ''Streptomyces coelicolor''. This antibiotic is a pH indicator that turns red under acidic conditions and blue under basic conditions, and was very helpful in isolating ''Streptomyces coelicolor'' organisms. Currently, actinorhodin alone is not used pharmaceutically, but the genes coding for actinorhodin production have been used recombinatorially in other species to form new antibiotic derivatives.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=12001Streptomyces coelicolor2007-05-31T04:06:49Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''. Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20) Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
(21) White, Janet and Mervyn Bibb. "''bldA'' Dependence of Undecylprodigiosin Production in ''Streptomyces coelicolor'' A3(2) Involves a Pathway-Specific Regulatory Cascade." (1999) <u>Journal of Bacteriology</u>. 179.3 p. 627-633. [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178740&blobtype=pdf Link to Article] <br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11999Streptomyces coelicolor2007-05-31T03:56:41Z<p>Afritch: /* Application to Biotechnology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''. Undecylprodigiosin, also known as Red because of its red color, is a type of prodiginine produced by ''Streptomyces coelicolor'' and is used as anti-tumor agent and an immunosupressant. Production of undecylprodigiosin is controlled by ''red'' genes.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20)Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11977Streptomyces coelicolor2007-05-31T03:31:12Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
(20)Wolpert, Manuel, Bertolt Gust, Bernd Kammerer and Lutz Heide. "Effects of deletions of ''mbtH''-like genes on clorobiocin biosynthesis in ''Streptomyces coelicolor''." (2007) Microbiology. 153. p. 1413-1423. [http://mic.sgmjournals.org/cgi/content/full/153/5/1413 Link to Article]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11976Streptomyces coelicolor2007-05-31T03:24:22Z<p>Afritch: /* Application to Biotechnology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
''Streptomyces'' species produce a majority of the antibiotics that have been discovered, so they are very importnat to biotechnology and the development of new antibiotics. ''Streptomyces coelicolor'' produces a number of different antibiotics, a few of which will be discussed here. Clorobiocin is an antibiotic that greatly inhibits DNA gyrase. It is not in use pharmacutically at this point, but it may be used as a starting material to make new antibiotics. Production of clorobiocin is controlled in part by the ''cloY'' gene, and is similar to a ''mtbH'' gene present in ''Mycobacterium tuberculosis''.<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11946Streptomyces coelicolor2007-05-31T01:21:07Z<p>Afritch: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
''Streptomyces coelicolor'' and other ''Streptomyces'' species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11945Streptomyces coelicolor2007-05-31T01:13:50Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Streptomyces coelicolor and other Streptomyces species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11943Streptomyces coelicolor2007-05-31T01:13:06Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Streptomyces coelicolor and other Streptomyces species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208.<br />
<br />
(19) "''Streptomyces coelicolor'' A3(2) Project at Sanger Institute." <u>Entrez Genome Project Website</u>. {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=242 Link to Website]<br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11940Streptomyces coelicolor2007-05-31T01:05:21Z<p>Afritch: /* Ecology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Streptomyces coelicolor and other Streptomyces species are important to soil environments because they are capapble of metabolizing other organism's remains. They are espescially important because they can degrade chitin and other compounds that are difficult to degrade.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. <br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11937Streptomyces coelicolor2007-05-31T00:53:51Z<p>Afritch: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<br />
(17) "''Streptomyces scabies''". <u>Wellcome Trust Sanger Institute</u>. [http://www.sanger.ac.uk/Projects/S_scabies/ Link to Website]<br />
<br />
(18) Zhang, Xiujun, Christopher A. Clark, and Gregg S. Pettis. "Interstrain Inhibition in the Sweet Potato Pathogen ''Streptomyces ipomoeae'': Purification and Characterization of a Highly Specific Bacteriocin and Cloning of Its Structural Gene". (2003) <u>Applied Environmental Microbiology</u>. 69.4 p. 2201-2208. <br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11934Streptomyces coelicolor2007-05-31T00:46:19Z<p>Afritch: /* Pathology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs, and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<references/><br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11933Streptomyces coelicolor2007-05-31T00:46:00Z<p>Afritch: /* Pathology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however, are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<references/><br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11931Streptomyces coelicolor2007-05-31T00:44:56Z<p>Afritch: /* Pathology */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
''Streptomyces coelicolor'' does not cause disease in humans, plants, or animals. Other ''Streptomyces'' species, however are plant pathogens. For example, ''Streptomyces scabies'' causes potato scabs and ''Streptomyces ipomoeae'' causes disease in sweet potatoes.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<references/><br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11898Streptomyces coelicolor2007-05-30T22:29:31Z<p>Afritch: /* Cell structure and metabolism */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
<br />
===Higher order taxa===<br />
<br />
Domain: Bacteria<br />
<br />
Phylum: Actinobacteria <br />
<br />
Class: Actinobacteria<br />
<br />
Subclass: Actinobacteridae <br />
<br />
Order: Actinomycetales<br />
<br />
Suborder: Streptomycineae <br />
<br />
Family: Streptomycetaceae<br />
<br />
Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. These indentations are the place where spores will form. The mosaic of fibers covering the aerial hyphae then form a ring around the indentations. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
<br />
<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
<br />
Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
<br />
''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<references/><br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritchhttps://microbewiki.kenyon.edu/index.php?title=Streptomyces_coelicolor&diff=11897Streptomyces coelicolor2007-05-30T22:25:55Z<p>Afritch: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification== <br />
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===Higher order taxa===<br />
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Domain: Bacteria<br />
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Phylum: Actinobacteria <br />
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Class: Actinobacteria<br />
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Subclass: Actinobacteridae <br />
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Order: Actinomycetales<br />
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Suborder: Streptomycineae <br />
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Family: Streptomycetaceae<br />
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Strains:<br />
''Streptomyces coelicolor'' A3(2)<br />
<br />
(1)[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI]<br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
===Genus=== <br />
Genus species: ''Streptomyces coelicolor''<br />
<br />
Other Names: ''Streptothrix coelicolor'', ''Cladothrix coelicolor'', ''Nocardia coelicolor'', ''Actinomyces coelicolor'' <br />
(1)<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Description and significance==<br />
''Streptomyces coelicolor'', a filamentous, high G-C, gram + bacteria, was first dubbed ''Streptothrix coelicolor'' in 1908 by R. Muller after he found it on a potato scab. Later, it became known as ''Streptomyces coelicolor''. ''Streptomyces coelicolor'', like the streptomyces genus in general, live in the soil. Streptomyces are responsible for much of the break down of organic material in the soil as well as the “earthy” smell of soil. They also live in colonies and have structural similarities to fungus. Colonies of ''Streptomyces coelicolor'' release pigments that are blue/green in alkali and red in acidic conditions, thereby giving the bacterial colonies those colors under the respective conditions.[[Image:Red_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
''Streptomyces'' colonies producing aerial mycelium, except for the red mutant colonies which are not http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html <br />
<br />
Other differentiating characteristics of ''Streptomyces coelicolor'' are grayish-yellow aerial mycelium, smooth spores, and no melanoid pigment(2). ''Streptomyces coelicolor'' are important bacteria and were sequenced because of their “adaptability to environmental stress”, “source of bioactive molecules for medicine and industry”, and “relat[ion] to human pathogens”(3). ''Streptomyces coelicolor'' has a very similar core genome to ''Mycobacterium tuberculosis'' and ''Corynebacterium diphtheriae'', as well as some similarity to ''Mycobacterium leprae'', so it can be used to study these disease causing bacteria. The streptomyces genus is responsible for producing a majority of the antibiotics in use today, as well as some immunosuppressants and anti-tumor agents. ''Streptomyces coelicolor'' also has an interesting life-cycle that includes differentiation into aerial mycelium and spore formation. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Genome structure==<br />
''Streptomyces coelicolor'' has one linear chromosome and two plasmids, one that is linear and one that is circular. The linear chromosome was sequenced from overlapping clones of the species, most of which were cosmids, that did not contain the two plasmids. This chromosome contains 8,667,507 base pairs, and was the largest bacterial genome sequenced at the time. (Since then, larger bacterial genomes have been sequenced.) The origin of replication (oriC) is located in the middle of the chromosome, and the ends of the chromosome contain terminal inverted repeats (TIRs). The 5’ terminal ends have proteins that are covalently bonded to them. Replication occurs in both directions leaving a gap in one strand of the new chromosome, which is patched by DNA synthesis. The chromosome is considered to be grouped into three regions – the core and two arms. The core region comprises about half of the chromosome and contains the essential genes for the survival of the organism, like “cell division, DNA replication, transcription, translation and amino-acid biosynthesis” (6). The two arm regions are different lengths, one about 1.5 MB and the other 2.3 MB long, and they code for nonessential functions like "secondary metabolites, hydrolytic exoenzymes, the conservons (conserved operons) and 'gas vesicle' proteins" (6). The SPC1 linear plasmid is 365,023 base pairs long, and is involved coding for some regulator proteins including three Sigma factors and proteins found on spore surfaces among other functions. The 31,317 base pair, circular plasmid, SPC2, has a stability region, replication origin, and transfer region. It has a relatively low copy number. <br />
<br />
Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Cell structure and metabolism==<br />
''Streptomyces coelicolor'' live in the soil, where nutrient conditions can change dramatically. As a result, this bacteria is capable of living on may different carbon sources including "glycerol, L-arabinose, D-arabitol, D-ribose, D-xylose, L-xylitol,<br />
D-fructose, D-galactose, D-gluconate, D-glucose, D-mannitol, D-mannose, L-rhamnose, salicin, cellobiose, lactose, maltose, melibiose, trehalose, acetate, citrate, lactate, malate, pyruvate, succinate, tartrate, propanoate, alanine, asparagine, glutamate, glycine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, tryptophan, [and] valine"(11). Some of its nitrogen sources are "aspartate, asparagine, glutamate, glutamine, isoleucine, leucine, lysine, praline, [and] valine"(11). Despite ''Streptomyces coelicolor'' ability to metabolize so many different food sources, it is only capable of aerobic respiration. The lactate dehydrogenase gene is present in Streptomyces coelicolor genome, so the organism should be able to obtain energy from fermentation, but it does not. Some theories as to why this occurs are that some of the other reactions necessary for survival depend on the presence of oxygen or that the byproducts of anaerobic respiration are toxic to the cells. The presence of nar genes, which code for respiratory nitrate reductaces, indicate that under oxygen limiting conditions, ''Streptomyces coelicolor'' should be able to use nitrate as an electron receptor. Researchers have determined that the nar genes are indeed expressed and probably used during growth in standing liquid where oxygen levels fluctuate. Despite these findings, conditions that would allow ''Streptomyces coelicolor'' to grow anaerobically in a lab setting have not been found yet. Metabolic changes in ''Streptomyces coelicolor'' also affect cell differentiation. For example, mutant strains lacking ''citA'', involved in citrate synthase coding, or some ''bld'' genes (discussed below) cannot form aerial mycelium when grown on glucose. Glucose forms acidogenic organic acids which makes the substrate in which the organism grows acidic. Citrate synthase initiates the TCA cycle which is necessary for acid metabolism, which is important in keeping the pH of the substrate at a level that does not prevent growth. Without the ''citA'' gene or some of the bld genes, this important ability in impaired and, as such, aerial mycelium and antibiotic production do not occur. When grown on mannitol, which is not acidogenic, aerial hyphae will form even in ''bld'' and ''citA'' mutants.<br />
<br />
''Streptomyces'' have a life cycle similar to that of fungi. The cycle starts with growth of vegetative mycelium from a spore, followed by ariel mycelium, and, then, spores. This complex life style is facilitated by cell differentiation. Instead of two totally separated cells forming after cell division, chains of cells remain linked together to form a branching “mycelium network”(14). Vegetative hyphae, the individual strands that make up the vegetative mycelium, have hydrophilic surfaces, which fit well since they usually grown in a moist region. When not grown in submerged culture, hyphae have an extra cellular matrix of up to 1.5 micrometers wide that surround it. Older hyphae have larger extra cellular layers than newer hyphae. Production of aerial mycelium is coded for in the ''bld'' genes of Streptomyces coelicolor. When grown in the presence of glucose, SapB is believed to help aerial mycelium break the surface tension of the liquid they begin growing in and ascend into the air. The surfaces of aerial hyphae, the individual strands that make up the aerial mycelium, are hydrophobic, unlike vegetative hyphae. A fibrous layer also surrounds newly formed aerial hyphae, and is believed to help break surface tension as the hyphae move out of an aqueous substrate and into the air. This fibrous layer is not present in older aerial hyphae, so it is believed to be replaced with a “more organized mosaic layer”(13). Sporulation in ''Streptomyces coelicolor'' is controlled by the ''whi'' genes. Sporulation begins when indentations at the tips of aerial hyphae begin to appear. The mosaic of fibers covering the aerial hyphae then form a ring around the place where the spore will form. A round spore then forms and is covered in the fibrous mosaic. Mature spores are denoted by surface concavities believed to be caused by metabolic slowing and dehydration.<br />
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Edited by Amy Stapp, student of Rachel Larsen at UCSD.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
Edited by Neena Patel, student of Rachel Larsen at UCSD.<br />
<br />
==Application to Biotechnology==<br />
[[Image:Blue_Streptomyces.jpg]] ''Image courtesy of John Innes Center Bioimaging'' [http://www.jic.ac.uk/corporate/index.htm JIC] <br />
<br />
"Colonies of ''Streptomyces coelicolor'' secreting blue actinorhodin antibiotic" ("From Mapping to Mining...", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==Current Research==<br />
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Research is being done to determine how ''Streptomyces coelicolor'' use signal transduction pathways to sense changes in their highly variable soil environments, which signals antibiotic and spore production. [http://bioweb2.bio.uea.ac.uk/faculty/HutchingsM.aspx Link to Researcher's Web-page]<br />
<br />
The bacterial development of ''Streptomyces coelicolor'' is also being studied to determine “the role of specific RNA polymerase holoenzymes controlling development and stress response, global characterisation of spore maturation and germination, cytoskeletal proteins, and chromosome organization during hyphal growth” (9). [http://bioweb2.bio.uea.ac.uk/faculty/KelemenG.aspx Link to Researcher's Web-Page]<br />
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''Streptomyces coelicolor'' is currently the subject of research at the University of Warwick due to its ability to produce prodiginines. These compounds show promise in targeting cancer cells, and a synthetic counterpart to the compound made naturally by ''Streptomyces coelicolor'' is in clinical trials as of November 2006.<br />
<br />
[[Image:Streptomyces_jewels.jpg]]''Image courtesy of the John Innes Center'' [http://www.jic.ac.uk/corporate/index.htm JIC]<br />
<br />
"Jewels in the crown of a Streptomyces colony are antibiotic secretions" ("From Mapping to Mining", John Innes Center) http://www.jic.bbsrc.ac.uk/SCIENCE/molmicro/Strept.html<br />
<br />
==References==<br />
(1) "''Streptomyces coelicolor'' A3(2)". <u>NCBI Taxonomy Browser</u>. 29 April 2007. [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=100226&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI].<br />
<br />
(2) Conn, Jean E. “The Pigment Production of ''Actinomyces coelicolor'' and ''A. violaceus-ruber''”. <u>Journal of Bacteriology</u>. 1943. Volume 46. p. 133-149. [http://jb.asm.org/cgi/reprint/46/2/133.pdf Link to Article]<br />
<br />
(3) “From Mapping to Mining the Streptomyces Genome”. <u>John Innes Centre Website</u>. 2001. [http://www.jic.ac.uk/corporate/about/publications/strept.pdf Link to Article]<br />
<br />
(4) Thompson, Charles J., Dorris Fink, and Liem D. Nguyen. “Principles of Microbial Alchemy: Insights from the ''Streptomyces coelicolor'' Genome Sequence”. <u>Genome Biology</u> 3.7. (2002) [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=139385&tools=bot Link to Article on PubMed]<br />
<br />
(5) Kutzner, Hans J and Selman A. Waksman. “''Streptomyces coelicolor'' Muller and ''Streptomyces violaceoruber'' Waksman and Curtis, Two Distinctly Different Organisms.” <u>Journal of Bacteriology</u> 78.4 (1959) p. 528-538. [http://jb.asm.org/cgi/reprint/78/4/528 Link to Article]<br />
<br />
(6) Bentley, S.D., K. F. Chater, A.-M. Cerdeño-Tárraga, G. L. Challis , N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.-H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.-A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill and D. A. Hopwood. "Complete Genome Sequence of the Model Actinomycete ''Streptomyces coelicolor'' A3(2)." <u>Nature</u>. 417. (2002) p. 141-147. [http://www.nature.com/nature/journal/v417/n6885/full/417141a.html Link to Article]<br />
<br />
(7) Bentley, S. D., S. Brown, L. D. Murphy, D. E. Harris, M. A. Quail, J. Parkhill, B. G. Barrell, J. R. McCormick, R. I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C. W. Chen, G. Chandra, D. Jakimowicz, H. M. Kieser, T. Kieser and K. F. Chater. "SPC1, a 356023 bp Linear Plasmid Adapted to the Ecology and Developmental Biology of It's Host, ''Streptomyces coelicolor''." <u>Molecular Microbiology</u> 51.6 (2004) p. 1615-1628.<br />
<br />
(8) Haug, Iris, Anke Weissenborn, Dirk Brolle, Stephen Bentley, Tobias Kieser, and Josef Altenbuchner. “Streptomyces Coelicolor A3(2) Plasmid SCP2*: Deductions from the Complete Sequence”. <u>Microbiology</u> 149 (2003). p. 505-513. [http://mic.sgmjournals.org/cgi/content/full/149/2/505 Link to Article]<br />
<br />
(9) “Streptomyces: Research.” 30 March 2007. UEA Norwich Website. University of East Anglia. 30 April 2007. http://openwetware.org/wiki/Streptomyces:Research <br />
<br />
(10) Stanley, Anna E., Laura J. Walton, Malek Kourdi Zerikly, Christophe Corre and Gregory L. Challis. “Elucidation of the ''Streptomyces coelicolor'' pathway to 4-methoxy-<br />
2,29-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine<br />
Biosynthesis.” <u>Chemical Communications Articles.</u> (Oct. 2006) RBS Publishing. p. 3981-3983. [http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b609556a&JournalCode=CC Link to Article]<br />
<br />
(11) Borodina, Irina, Preben Krabben, and Jens Nielsen. "Genome-scale Analysis of Streptomyces Coelicolor A3(2) Metabolism". <u>Genome Research</u>. 15 (June 2005) p. 820-828.<br />
<br />
(12) Keleman, Gabriella H. and Mark J. Buttner. "Initiation of aerial mycelium formation in Streptomyces". <u>Current Opinion in Microbiology</u>. 1 (1998) p. 656-662.<br />
<br />
(13) Del Sol, Ricardo, Ian Armstrong, Chris Wright, and Paul Dyson. “Characterization of Changes to the Cell Surface during the Life Cycle of Streptomyces coelicolor: Atomic Force Microscopy of Living Cells.” (2007) <u>Journal of Bacteriology</u>. 189.6 p. 2219-2225.<br />
<br />
(14) “Cell Division and Development of Streptomyces”. <u>Genexpress</u>. 22 Aug. 2002. Scheikunde University Leiden. 29 May 2007. [http://wwwchem.leidenuniv.nl/genexpress/ie/vanwezel/vanwezel.htm Link to Website] <br />
<br />
(15) Viollier, Patrick H., Wolfgang Minas, Glenn E. Dale, Marc Folcher, and Charles J. Thompson. "Role of Acid Metabolism in Streptomyces coelicolor Morphological Differentiation and Antibiotic Biosynthesis." (2001) <u>Journal of Bacteriology</u>. 183.10 <br />
p. 3184-3192.<br />
<br />
(16) van Keulen, G., J. Alderson, J. White and R.G. Sawers. "Nitrate Respiration in the actinomycete ''Streptomyces coelicolor''." (2005) <u>Biochemical Society Transactions</u>. 33.1 p.210 - 212. <br />
<references/><br />
<br />
<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Afritch