Thermofilum pendens: Difference between revisions
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==Description and significance== | ==Description and significance== | ||
Thermofilum pendens was first isolated from a solfataric hot spring in Iceland in the early 1980s (1). Since its discovery, T. pendens have also been isolated in solfatara environments. Thus, this archeabacteria can sustain life in a hot and slightly acidic environment making it a hyperthermophile and acidophile, or a thermoacidophile (2). Its optimum growth conditions are 85-90 degree C with a pH of 5-6 and 0.1 – 2% salinity (3, 7). Being an archea, T. pendens has the ability to provide heat resistance enzymes which can be applied in biotechnology. | Thermofilum pendens was first isolated from a solfataric hot spring in Iceland in the early 1980s by Wolfram Zillig (1,10). Since its discovery, T. pendens have also been isolated in solfatara environments, such as Yellowstone National Park (U.S.) and Vulcano Island (Italy). Thus, this archeabacteria can sustain life in a hot and slightly acidic environment making it a hyperthermophile and acidophile, or a thermoacidophile (2). Its optimum growth conditions are 85-90 degree C with a pH of 5-6 and 0.1 – 2% salinity (3, 7). However, it has been found in sites with temperature ranging from 67 -93 degree C and pH ranging from 2.8 - 7.6 (9). Being an archea, T. pendens has the ability to provide heat resistance enzymes which can be applied in biotechnology. | ||
Furthermore, T. pendens is important to the evolutionary process because it the deepest branching lineage to the Eukaryote domain (6). According to a parsimonious phylogenetic tree for 16S rRNA, T. pendens is the out-group of the Crenarchaeota making it the closest evolutionary branch to the Eurakyota domain (7,9). | |||
Furthermore, T. pendens is important to the evolutionary process because it the deepest branching lineage to the Eukaryote domain (6). According to a parsimonious phylogenetic tree for 16S rRNA, T. pendens is the out-group of the Crenarchaeota making it the closest evolutionary branch to the Eurakyota domain (7,9). In addition, it is one of four Crenarchaeota species sequenced. Thus, T. pendens provide the ideal genome for comparative studies to distinguish between Thermoproteales from other Crenarchaeotes (1). | |||
==Genome structure== | ==Genome structure== | ||
Thermofilum pendens has a circular chromosome with 1,781,889 base pairs. Out of the 1.8 Mbp, 57.67 % is G+C content, which is equivalent to 1,027,615 base pairs. It has 1,879 genes in the chromosome and 1,824 genes are protein coding and 40 are structural RNA. It also has one sequenced plasmid with 31,504 base pairs; of which 56.5% is GC content (2). The importance of the plasmid is not yet known. | |||
==Cell structure and metabolism== | ==Cell structure and metabolism== | ||
T. pendens is a Gram negative, rod-shaped, non-motile, anaerobic organism. It has an S-layer surrounding the cytoplasmic membrane. During cell division, T. pendens will bud and septum formation does not occur. It is within the Thermofilaceae family which have the general shape of a thin rod, between 0.15 to 0.35 μm in diameter and 1 to >100 μm in length. An interesting feature of this organism is it has a long filamentous structure which can be 100 mm in length (3). However, out of the 9 member of the Genera, Thermofilum is the smallest. Hence, it can be difficult to recognize under the phase contrast light microscope (11). The cell membrane of Thermofilum, as well as other thermophilic archaebacteria, is found to have C20 phytanyl chains and C40 biphytanyl chains. Glycerol-dialkyl-glycerol-tetraethers, aka GDGT, is bridged by two sn-2,3-glycerol moieties through ether linkages by two isoprenoid C40 diols (4). This allows for cell stability in high heat. | |||
Metabolism | |||
This organism is heterotrophic and uses Sulfur, through complex organic compounds, to gain energy (2, 3). Elemental sulfur and peptides, from polar lipid of T. tenax, is reduced yielding CO2 and H2S (3). Polar lipid is assume to be rich in sulfur which is most likely broken down and converted into energy. Since T. pendens is an older organism, according to the parsimonious phylogenetic tree, its metabolism is not one of the best. Converting elemental sulfur can only yield a maximum of 27 kJ/mol e- (9). | |||
==Ecology== | ==Ecology== | ||
There is little information about T. Pendens and its interaction with other organism. One piece of vital information is T. pendens growth is dependent on a polar lipid extract of T. tenax (1, 13). However, another closely related species, Thermofilum librum, is independent of this polar lipid extract (13). For more information see Metabolism. | |||
==Pathology== | ==Pathology== | ||
Currently, this organism is not pathogenic. | |||
==Application to Biotechnology== | ==Application to Biotechnology== | ||
T. pendens, like other thermophile archaea, have heatstable enzymes that can potentially be used for industrial processes and research. Some of these enzymes are amylases, proteases, dehydrogenase, oxidoreductases and DNA polymerases. When the enzymes are cloned and used in mesophilic hosts, the thermophilic properties is retained, meaning the properties are genetically coded. As the number of genome sequenced increase, an increase in potential use for different biotechnological applications ensues (7). Furthermore, T. pendens are anaerobes with potential use for organic waste treatment or fuel production systems. Research in this area is still being conducted at this moment (3). | |||
==Current Research== | ==Current Research== | ||
Once again, T. pendens is the most deeply branching member of the Crenarchaeota Kingdom; thus, its genomes allow for better studies on genes differentiation between Thermoprotealees and Crenarchaeotes (1, 6). Additionally, T. pendens have a large variable loop which may hint evolutionary processes. The variable loop is 18 nucleotides long within the precursor tRNAGly. A new theory in which larger variable loop (type II) cam from smaller variable loop (type I) by retaining a splicing-deficient intron is proposed by Kjem J. et al. research (5). Recent studies have found most of eurakyotic tDNA introns to be located in anticodon loops between nucleotides positions 37 and 38, or canonical position. However, archaeal tDNA introns are found at noncanonical positions. In an attempt to better predict multiple introns in tRNA, SPLITS was developed and later upgraded to SPLITSX. T. Pendens is one of the candidates having multiple introns. So far, all candidates only exist in archaeal cells (14). | |||
==References== | ==References== | ||
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< http://mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000453/current/pdf>. | < http://mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000453/current/pdf>. | ||
8) Burggraf S., Huber H. Stetter K. O. “Reclassification of the Crenarchaeal Orders and Families in Accordance with 16S rRNA Sequence | 8) Burggraf S., Huber H. Stetter K. O. “Reclassification of the Crenarchaeal Orders and Families in Accordance with 16S rRNA Sequence | ||
Data”. Internation Journal of Systematic Bacteriology. July 1997. p. 657 -660. < http://ijs.sgsmjournals.org/cgi/reprint/47/3/657.pdf>. | |||
9) Rogers K., Amend J. “Archaeal diversity and geochemical energy yields in a geothermal well on Vulcano Island, Italy”. Geobiology. December 2005. p. 319-332. < http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1472-4669.2006.00064.x?cookieSet=1>. | |||
10) Pfeifer, F. “Wolfram Zillig (1925 – 2005)”. SpringerLink. 23 September 2005. | |||
< http://www.springerlink.com/content/p511875481375256/fulltext.html>. | |||
11) Knoll A., Osborn M., Baross J., Berg H., Pace N., Sogin M. “Size Limits of Very Small Microorganisms: Proceedings of a Workshop”. Space Studies Board. 1999. | |||
12) Vieille C., Zeikus G. “Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability”. American Society for Microbiology – Microbiology and Molecular Biology Reviews. March 2001. p. 1-43. | |||
13) Itoh T., Suzuki K., Sanchez P., Nakase T. “Caldivirga maquilingensis gen. nov., sp. nov., a | |||
new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines”. International Journal of Systematic Bacteriology. 1999. p. 1157-1163. | |||
14) Sugahara J., Yachie N., Arakawa K., Tomita M. “In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs”. Cold Spring Harbor Laboratory Press. March 16, 2007. <http://www.rnajournal.org/cgi/content/full/13/5/671>. | |||
Edited by Quan Pham student of [mailto:ralarsen@ucsd.edu Rachel Larsen] | Edited by Quan Pham student of [mailto:ralarsen@ucsd.edu Rachel Larsen] | ||
Latest revision as of 03:36, 20 August 2010
A Microbial Biorealm page on the genus Thermofilum pendens
Classification
Higher order taxa
Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermofilaceae [Others may be used. Use NCBI link to find]
Species
|
NCBI: Taxonomy |
Thermofilum pendens, Thermofilum pendens Hrk 5
Description and significance
Thermofilum pendens was first isolated from a solfataric hot spring in Iceland in the early 1980s by Wolfram Zillig (1,10). Since its discovery, T. pendens have also been isolated in solfatara environments, such as Yellowstone National Park (U.S.) and Vulcano Island (Italy). Thus, this archeabacteria can sustain life in a hot and slightly acidic environment making it a hyperthermophile and acidophile, or a thermoacidophile (2). Its optimum growth conditions are 85-90 degree C with a pH of 5-6 and 0.1 – 2% salinity (3, 7). However, it has been found in sites with temperature ranging from 67 -93 degree C and pH ranging from 2.8 - 7.6 (9). Being an archea, T. pendens has the ability to provide heat resistance enzymes which can be applied in biotechnology.
Furthermore, T. pendens is important to the evolutionary process because it the deepest branching lineage to the Eukaryote domain (6). According to a parsimonious phylogenetic tree for 16S rRNA, T. pendens is the out-group of the Crenarchaeota making it the closest evolutionary branch to the Eurakyota domain (7,9). In addition, it is one of four Crenarchaeota species sequenced. Thus, T. pendens provide the ideal genome for comparative studies to distinguish between Thermoproteales from other Crenarchaeotes (1).
Genome structure
Thermofilum pendens has a circular chromosome with 1,781,889 base pairs. Out of the 1.8 Mbp, 57.67 % is G+C content, which is equivalent to 1,027,615 base pairs. It has 1,879 genes in the chromosome and 1,824 genes are protein coding and 40 are structural RNA. It also has one sequenced plasmid with 31,504 base pairs; of which 56.5% is GC content (2). The importance of the plasmid is not yet known.
Cell structure and metabolism
T. pendens is a Gram negative, rod-shaped, non-motile, anaerobic organism. It has an S-layer surrounding the cytoplasmic membrane. During cell division, T. pendens will bud and septum formation does not occur. It is within the Thermofilaceae family which have the general shape of a thin rod, between 0.15 to 0.35 μm in diameter and 1 to >100 μm in length. An interesting feature of this organism is it has a long filamentous structure which can be 100 mm in length (3). However, out of the 9 member of the Genera, Thermofilum is the smallest. Hence, it can be difficult to recognize under the phase contrast light microscope (11). The cell membrane of Thermofilum, as well as other thermophilic archaebacteria, is found to have C20 phytanyl chains and C40 biphytanyl chains. Glycerol-dialkyl-glycerol-tetraethers, aka GDGT, is bridged by two sn-2,3-glycerol moieties through ether linkages by two isoprenoid C40 diols (4). This allows for cell stability in high heat.
Metabolism
This organism is heterotrophic and uses Sulfur, through complex organic compounds, to gain energy (2, 3). Elemental sulfur and peptides, from polar lipid of T. tenax, is reduced yielding CO2 and H2S (3). Polar lipid is assume to be rich in sulfur which is most likely broken down and converted into energy. Since T. pendens is an older organism, according to the parsimonious phylogenetic tree, its metabolism is not one of the best. Converting elemental sulfur can only yield a maximum of 27 kJ/mol e- (9).
Ecology
There is little information about T. Pendens and its interaction with other organism. One piece of vital information is T. pendens growth is dependent on a polar lipid extract of T. tenax (1, 13). However, another closely related species, Thermofilum librum, is independent of this polar lipid extract (13). For more information see Metabolism.
Pathology
Currently, this organism is not pathogenic.
Application to Biotechnology
T. pendens, like other thermophile archaea, have heatstable enzymes that can potentially be used for industrial processes and research. Some of these enzymes are amylases, proteases, dehydrogenase, oxidoreductases and DNA polymerases. When the enzymes are cloned and used in mesophilic hosts, the thermophilic properties is retained, meaning the properties are genetically coded. As the number of genome sequenced increase, an increase in potential use for different biotechnological applications ensues (7). Furthermore, T. pendens are anaerobes with potential use for organic waste treatment or fuel production systems. Research in this area is still being conducted at this moment (3).
Current Research
Once again, T. pendens is the most deeply branching member of the Crenarchaeota Kingdom; thus, its genomes allow for better studies on genes differentiation between Thermoprotealees and Crenarchaeotes (1, 6). Additionally, T. pendens have a large variable loop which may hint evolutionary processes. The variable loop is 18 nucleotides long within the precursor tRNAGly. A new theory in which larger variable loop (type II) cam from smaller variable loop (type I) by retaining a splicing-deficient intron is proposed by Kjem J. et al. research (5). Recent studies have found most of eurakyotic tDNA introns to be located in anticodon loops between nucleotides positions 37 and 38, or canonical position. However, archaeal tDNA introns are found at noncanonical positions. In an attempt to better predict multiple introns in tRNA, SPLITS was developed and later upgraded to SPLITSX. T. Pendens is one of the candidates having multiple introns. So far, all candidates only exist in archaeal cells (14).
References
1) Richardson P., Anderson I., Woese C., Olsen G., Reich C. “Thermofilum pendens Hrk 5: finished genome”. JGI (Joint Genome Institute). <http://genome.jgi-psf.org/finished_microbes/thepe/thepe.home.html>.
2) NCBI. “Thermofilum pendens Hrk 5 project at DOE Joint Genome Institute”. <http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16331>.
3) Lowe S., Jain M., Zeikus G., “Biology, Ecology, and Biotechnological Applications of Anaerobic Bacteria Adapted to Environmental Stresses in Temperature, pH, Salinity, or Substrates”. American Society for Microbiology – Microbiological Reviews. June, 1993. p. 451-509.
4) Rosa M., Gambacorta A., Gliozzi A. “Structure, Biosynthesis, and Physicochemical Properties of Archaebacterial Lipids”. American Society for Microbiology – Microbiological Reviews. March 1986. p. 70-80.
5) Kjems, J., Leffers H., Olesen T., Garrett R. “A Unique tRNA Intron in the Variable Loop of the Extreme Thermophile Thermofilum pendens and Its Possible Evolutionary Implications”. The American Society for Biochemistry and Molecular Biology – The Journal of Biological Chemistry. October 25, 1989.
6) Gao B., Gupta R. “Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis”. Biomed Central Genomics. 29 March 2007.
7) Huber, Harald. “Crenarchaeota”. Wiley InterScience – Encyclopedia of Life Sciences. April 24, 2006. < http://mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000453/current/pdf>.
8) Burggraf S., Huber H. Stetter K. O. “Reclassification of the Crenarchaeal Orders and Families in Accordance with 16S rRNA Sequence Data”. Internation Journal of Systematic Bacteriology. July 1997. p. 657 -660. < http://ijs.sgsmjournals.org/cgi/reprint/47/3/657.pdf>.
9) Rogers K., Amend J. “Archaeal diversity and geochemical energy yields in a geothermal well on Vulcano Island, Italy”. Geobiology. December 2005. p. 319-332. < http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1472-4669.2006.00064.x?cookieSet=1>.
10) Pfeifer, F. “Wolfram Zillig (1925 – 2005)”. SpringerLink. 23 September 2005. < http://www.springerlink.com/content/p511875481375256/fulltext.html>.
11) Knoll A., Osborn M., Baross J., Berg H., Pace N., Sogin M. “Size Limits of Very Small Microorganisms: Proceedings of a Workshop”. Space Studies Board. 1999.
12) Vieille C., Zeikus G. “Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability”. American Society for Microbiology – Microbiology and Molecular Biology Reviews. March 2001. p. 1-43.
13) Itoh T., Suzuki K., Sanchez P., Nakase T. “Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines”. International Journal of Systematic Bacteriology. 1999. p. 1157-1163.
14) Sugahara J., Yachie N., Arakawa K., Tomita M. “In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs”. Cold Spring Harbor Laboratory Press. March 16, 2007. <http://www.rnajournal.org/cgi/content/full/13/5/671>.
Edited by Quan Pham student of Rachel Larsen
