https://microbewiki.kenyon.edu/api.php?action=feedcontributions&user=Landonguyen&feedformat=atommicrobewiki - User contributions [en]2024-03-28T16:15:55ZUser contributionsMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16910Methylobacillus flagellatus2007-06-05T08:06:55Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
Note: Please refer to citation #3 for an image (courtesy of Trotsenko and Doronina) of Methylobacillus flagellatus KT strain. <br />
<br />
<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
Joe Bischoff, Mikhail Domrachev, Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov, Richard Sternberg, Sean Turner.<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16842Methylobacillus flagellatus2007-06-05T07:47:03Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
Note: Please refer to citation #3 for an image (courtesy of Trotsenko and Doronina) of Methylobacillus flagellatus KT strain. <br />
<br />
<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16827Methylobacillus flagellatus2007-06-05T07:43:19Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
Note: Please refer to citation #3 for an image of Methylobacillus flagellatus KT strain.<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16821Methylobacillus flagellatus2007-06-05T07:41:39Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16813Methylobacillus flagellatus2007-06-05T07:40:27Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16803Methylobacillus flagellatus2007-06-05T07:38:19Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
<br />
==Genome structure==<br />
<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16795Methylobacillus flagellatus2007-06-05T07:37:11Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
<br />
==Genome structure==<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
<br />
Metabolism-<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=16787Methylobacillus flagellatus2007-06-05T07:35:12Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
Methylobacillus is a group of methylotrophic anaerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. (2, 4)These organisms are one of Earth’s most important carbon recycler, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. (1, 2) “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” (6) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” (1) The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (2) “M. flagellatus is most closely related to other members of the family Methylophilaceae.” (2) The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (3) Using small-subunit 16S rRNAs (1) and comparing metabolic/ phylogenic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). (2)<br />
<br />
<br />
==Genome structure==<br />
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. (2)<br />
<br />
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. (2)<br />
Note: The authors did not specify the full name of CRISPR. They just provided the acronym.<br />
<br />
<br />
<br />
<br />
==Ecology==<br />
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. (13) Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, where as Methylobacillus pratensis were isolated from meadow grass. (2, 13) The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.<br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. (7) The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. (7) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, (1) and “may contribute more [than carbon dioxide] to global warming.” (1)<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (5) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (2) These compounds can range from heterologous proteins and amino-acids to vitamins. (6) Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(6) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (7) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. (9)<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(6) Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (7) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. (6)<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively indicated that M. flagellatus is closely related to members of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. (2) A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
<br />
<br />
Metabolism-<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) [a key enzyme of the cyclic oxidation pathway], and methenyl H4MPT cyclohydrolase (CH) [participating in the direct oxidation of formaldehyde via H4MPT derivatives] (10), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates” (10), and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” (10)<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this [linear oxidation] pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” (10) The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, where as Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” (10)<br />
<br />
<br />
<br />
==References==<br />
Bonnie Jo Bratina, Gregory A. Brusseau, Richard S. Hanson. “Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM, Lidstrom ME. “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
Siddiqui AA, Jalah R, Sharma YD. “Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
Marchenko GN, Marchenko ND, Tsygankov YD, Chistoserdov AY. “Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282. (5)<br />
==========================================================<br />
Richard S. Hanson, Thomas E. Hanson. “Methanotrophic bacteria” Microbiological Reviews. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
Kiyoshi Tsuji, H. C. Tsien, R. S. Hanson, S. R. DePalma, R. Scholtz, S. LaRoche. “16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
Baev M V, Chistoserdova L V, Polanuer B M, et al. “Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Archives of Microbiology. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
Chongcharoen R, Smith TJ, Flint KP, Dalton H. “Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME.<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
Kalyuzhnaya MG, Zabinsky R, Bowerman S, Baker DR, Lidstrom ME, Chistoserdova L.<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006. Vol 72, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
Doronina, Nina V.; Trotsenko, Yuri A.; Kolganova, Tatjana V., et al. “Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457. (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=14586Methylobacillus flagellatus2007-06-04T21:48:28Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus KT strain''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
<br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
==========================================================<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=14585Methylobacillus flagellatus2007-06-04T21:46:35Z<p>Landonguyen: /* References */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
<br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
==========================================================<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
==========================================================<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
==========================================================<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
==========================================================<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
==========================================================<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
==========================================================<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
==========================================================<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
==========================================================<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
==========================================================<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
==========================================================<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
==========================================================<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
==========================================================<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=14582Methylobacillus flagellatus2007-06-04T21:38:47Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
<br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13934Methylobacillus flagellatus2007-06-04T07:19:15Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
<br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
<br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus’ is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13892Methylobacillus flagellatus2007-06-04T06:57:26Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus’ is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13889Methylobacillus flagellatus2007-06-04T06:56:55Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
Genomic analysis-<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus’ is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13885Methylobacillus flagellatus2007-06-04T06:53:49Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Methylobacillus flagellatus''<br />
<br />
==Description and significance==<br />
<br />
(2, 4) Methylobacillus is a group of methylotrophic anaerobic bacteria, and they are known to be abundant in marine and fresh water ecosystems. (1, 2)These organisms play a huge role in the recycling of carbon compounds (i.e.: methane, methanol, and methylated amines) on Earth. (1) Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. (6) In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs. (1) According to Bonnie et al, methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years. The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.<br />
(2) One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in a metropolitan sewer system (3) M. flagellatus belongs to the family Methylophilaceae. The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. (1) Using small-subunit 16S rRNAs (2) and comparing metabolic/ phylogenetic similarities and differences (2) between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). <br />
<br />
<br />
==Genome structure==<br />
<br />
(2) The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins.(2) According to Chistoserdova et al, M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). (2) The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs.(2) The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. <br />
(2) Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs representing direct repeats. (2) Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. (2) The most interesting aspect relates to a region in the genome named CRISPR.(2) This region of the genome has not been fully studied, but there are strong evidences linking this region to lateral gene transfer, host cell defense, replication, and regulation. <br />
<br />
==Ecology==<br />
<br />
(13) A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus, and Methylovorus as terrestrial (land and fresh-water) methylobacteria. (13) While marine obligate methylotrophs are assigned to the genus Methylophaga. <br />
As we have mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. (7) Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms. (7) A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlook, because without these methanotrophs the vast majority of atmospheric methane would not be degraded. (1) The accumulation of methane gas would cause the Earth’s temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.”<br />
<br />
==Pathology==<br />
<br />
No known pathogenic quality of M. flagellatus has been discovered.<br />
<br />
==Application to Biotechnology==<br />
(5) Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass (2) allows for practical applications such as inexpensive industrial productions of commercially needed compounds. (6) These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials;(6) they use these carbon sources to fulfill their energy and carbon requirements.(7) As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). (9) Another common environmental pollutant that results from industrial processes is formaldehyde. (9) Recently a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes.<br />
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. (6) Methanotrophs are a subset of a physiological group of methylotrophs,(6) and its sole assimilatory/dissmilatory carbon source is methane.(7) Methanotrophs also possess MMO, and this enzyme has a broad substrate specificity and catalyzes the oxidation of a wide variety of water pollutants such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. (6) MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs.<br />
<br />
==Current Research==<br />
<br />
Genomic analysis-<br />
An article named “Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” that was recently published in the Journal of Bacteriology gave us a better understanding on the genome of M. flagellatus. Chistoserdova et al. reported that M. flagellatus’ genome closely matched some of the predictions set forth by other researchers. The genomic data conclusively catergorized M. flagellatus as a member of the Methylophilaceae family. Most of the genes encoded in the M. flagellatus genome are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. Chistoserdova et al. also proved that M. flagellatus’ is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. (2) One last notable point to mention is that the M. flagellatus’ genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. A general self conjecture is that the absence of these self-defense mechanisms would help explain why M. flagellatus has no pathogenic qualities.<br />
<br />
Population survey/detection methods-<br />
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” (11) The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” (11) Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method’s effectiveness.<br />
<br />
Metabolism-<br />
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, (10) “generation of reduced cofactors for biosynthetic purposes”, and, or formaldehyde detoxification.<br />
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd), a key enzyme of the cyclic oxidation pathway, and methenyl H4MPT cyclohydrolase (CH), (10) “participating in the direct oxidation of formaldehyde via H4MPT derivatives”, Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests (10) “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically (10) “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway.”<br />
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus (10) “mutants defective in this pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures,” the result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde. Where as Methylobacterium extorquens uses this pathway as its (10) “main energy-generating pathway for methylotrophic growth.”<br />
<br />
<br />
<br />
==References==<br />
“Use of 16S rRNA analysis to investigate phylogeny of methylotrophic bacteria” International Journal of Systematic Bacteriology. 1992. Vol 42, No. 4. p. 645-648. (1)<br />
<br />
“Genome of Methylobacillus flagellatus, Molecular Basis for Obligated Methylotrophy, and Polyphyletic Origin of Methylotrophy” American Society for Microbiology. 2007. Vol 189, No.11. p. 4020-4027. (2)<br />
<br />
http://genome.jgi-psf.org/draft_microbes/metfl/metfl.home.html (3)<br />
<br />
“Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus” Journal of biochemical and biophysical methods. 2007. Vol 70, No.4. p. 539-546. (4)<br />
<br />
“Organization of threonine biosynthesis genes from the obligate methylotroph Methylobacillus flagellatus” Microbiology. 1999. Vol 145, No.11. p. 3273-3282 (5)<br />
<br />
“Methanotrophic bacteria” American Society for Microbiology. 1996. Vol 60, No. 2. p. 439-471. (6)<br />
<br />
“16s ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs” Journal of General Microbiology. 1990. Vol 136. No. not available. p. 1-10. (7)<br />
<br />
“Effect of formaldehyde on growth of obligate methylotroph Methylobacillus flagellatum in a substrate non-limited continuous culture” Arch Microbiol. 1992. Vol 158, No. not available. p. 145-148. (8)<br />
<br />
“Adaptation and acclimatization to formaldehyde in methylotrophs capable of high-concentration formaldedyde detoxification” Microbiology. 2005. Vol 151. No. not available. p.2615-2622. (9)<br />
<br />
“Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph” Microbiology. 2000. Vol 146. No. 1. p. 233-238. (10)<br />
<br />
“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations” Applied and Environmental Microbiology. 2006, No. 6. p. 4293-4301. (11)<br />
<br />
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=405&lvl=3&lin=f&keep=1&srchmode=1&unlock (12)<br />
<br />
“Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass” International Journal of Systematic and Evolutionary Microbiology. 2004. Vol 54. No. not available. p. 1453-1457 (13)</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13881Methylobacillus flagellatus2007-06-04T06:51:08Z<p>Landonguyen: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
(12) Bacteria; Proteobacteria; b-Proteobacteria; Methylophilaes; Methylophilaceae; Methylobacillus; Methylobacillus flagellatus<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Thermoplasma volcanium''<br />
<br />
==Description and significance==<br />
<br />
Thermoplasma volcanium can be isolated from coal refuse piles, solfatara fields, and hot springs. This microbe is thermophilic and acidophilic. It lives in a high temperature environment in the range of 33˚C to 67˚C with the optimum at 60˚C. Even though it survives at this high temperature, it is still the lowest among archaea. Additionally, it only survives in acidic environment with pH between 1.0 and 4.0, with the optimum at pH of 2.0. Thermoplasma cells lyse at neutral pH. Research has shown that Thermoplasma volcanium may be the host cell of the endosymbrosis theory of eukaryotic cells. Hence, the genome is sequenced to confirm this hypothesis.<br />
<br />
==Genome structure==<br />
<br />
Thermoplasma volcanium has a circular DNA with 1,584,804 nucleotides. It does not contain any plasmids. However, it possesses about 70 proteins not found in any other archaea’s genome.<br />
<br />
==Cell structure and metabolism==<br />
<br />
This microbe has a unique cell membrane that contains tetraether lipids. It lacks any kind of cell wall, which causes it to have irregular shapes and is capable of assuming different shapes. The microbe uses multiple flagella for high motility. <br />
Thermoplasma volcanium is heterotrophic and therefore requires it to obtain nutrients from other organisms especially those who cannot survive in acidic or high temperature environments. Depending on its living conditions, the microbe is both anaerobic and aerobic. It is anaerobic in the presence of elemental sulfur.<br />
<br />
==Ecology==<br />
<br />
Due to its evolutionary ties to eukaryotes, Thermoplasma genus can be used as model organism for researches.<br />
<br />
==Pathology==<br />
<br />
There is no known pathogen among different strains of Thermoplasma volcanium.<br />
<br />
==Application to Biotechnology==<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Methylobacillus_flagellatus&diff=13876Methylobacillus flagellatus2007-06-04T06:49:06Z<p>Landonguyen: New page: {{Biorealm Genus}} ==Classification== ===Higher order taxa=== Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmataceae; Thermoplasma ===Species=== {| | height="10" bgcolor="#FFDF95"...</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmataceae; Thermoplasma<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Thermoplasma volcanium''<br />
<br />
==Description and significance==<br />
<br />
Thermoplasma volcanium can be isolated from coal refuse piles, solfatara fields, and hot springs. This microbe is thermophilic and acidophilic. It lives in a high temperature environment in the range of 33˚C to 67˚C with the optimum at 60˚C. Even though it survives at this high temperature, it is still the lowest among archaea. Additionally, it only survives in acidic environment with pH between 1.0 and 4.0, with the optimum at pH of 2.0. Thermoplasma cells lyse at neutral pH. Research has shown that Thermoplasma volcanium may be the host cell of the endosymbrosis theory of eukaryotic cells. Hence, the genome is sequenced to confirm this hypothesis.<br />
<br />
==Genome structure==<br />
<br />
Thermoplasma volcanium has a circular DNA with 1,584,804 nucleotides. It does not contain any plasmids. However, it possesses about 70 proteins not found in any other archaea’s genome.<br />
<br />
==Cell structure and metabolism==<br />
<br />
This microbe has a unique cell membrane that contains tetraether lipids. It lacks any kind of cell wall, which causes it to have irregular shapes and is capable of assuming different shapes. The microbe uses multiple flagella for high motility. <br />
Thermoplasma volcanium is heterotrophic and therefore requires it to obtain nutrients from other organisms especially those who cannot survive in acidic or high temperature environments. Depending on its living conditions, the microbe is both anaerobic and aerobic. It is anaerobic in the presence of elemental sulfur.<br />
<br />
==Ecology==<br />
<br />
Due to its evolutionary ties to eukaryotes, Thermoplasma genus can be used as model organism for researches.<br />
<br />
==Pathology==<br />
<br />
There is no known pathogen among different strains of Thermoplasma volcanium.<br />
<br />
==Application to Biotechnology==<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=User_talk:Landonguyen&diff=13866User talk:Landonguyen2007-06-04T06:44:31Z<p>Landonguyen: Methylobacillus flagellatus KT</p>
<hr />
<div>== Methylobacillus flagellatus KT ==<br />
<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmataceae; Thermoplasma<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Thermoplasma volcanium''<br />
<br />
==Description and significance==<br />
<br />
Thermoplasma volcanium can be isolated from coal refuse piles, solfatara fields, and hot springs. This microbe is thermophilic and acidophilic. It lives in a high temperature environment in the range of 33˚C to 67˚C with the optimum at 60˚C. Even though it survives at this high temperature, it is still the lowest among archaea. Additionally, it only survives in acidic environment with pH between 1.0 and 4.0, with the optimum at pH of 2.0. Thermoplasma cells lyse at neutral pH. Research has shown that Thermoplasma volcanium may be the host cell of the endosymbrosis theory of eukaryotic cells. Hence, the genome is sequenced to confirm this hypothesis.<br />
<br />
==Genome structure==<br />
<br />
Thermoplasma volcanium has a circular DNA with 1,584,804 nucleotides. It does not contain any plasmids. However, it possesses about 70 proteins not found in any other archaea’s genome.<br />
<br />
==Cell structure and metabolism==<br />
<br />
This microbe has a unique cell membrane that contains tetraether lipids. It lacks any kind of cell wall, which causes it to have irregular shapes and is capable of assuming different shapes. The microbe uses multiple flagella for high motility. <br />
Thermoplasma volcanium is heterotrophic and therefore requires it to obtain nutrients from other organisms especially those who cannot survive in acidic or high temperature environments. Depending on its living conditions, the microbe is both anaerobic and aerobic. It is anaerobic in the presence of elemental sulfur.<br />
<br />
==Ecology==<br />
<br />
Due to its evolutionary ties to eukaryotes, Thermoplasma genus can be used as model organism for researches.<br />
<br />
==Pathology==<br />
<br />
There is no known pathogen among different strains of Thermoplasma volcanium.<br />
<br />
==Application to Biotechnology==<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=User:Landonguyen&diff=13861User:Landonguyen2007-06-04T06:43:36Z<p>Landonguyen: Removing all content from page</p>
<hr />
<div></div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=User:Landonguyen&diff=13858User:Landonguyen2007-06-04T06:41:43Z<p>Landonguyen: </p>
<hr />
<div>CLASSICFICATION<br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
===Higher order taxa===<br />
<br />
Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmataceae; Thermoplasma<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Thermoplasma volcanium''<br />
<br />
==Description and significance==<br />
<br />
Thermoplasma volcanium can be isolated from coal refuse piles, solfatara fields, and hot springs. This microbe is thermophilic and acidophilic. It lives in a high temperature environment in the range of 33˚C to 67˚C with the optimum at 60˚C. Even though it survives at this high temperature, it is still the lowest among archaea. Additionally, it only survives in acidic environment with pH between 1.0 and 4.0, with the optimum at pH of 2.0. Thermoplasma cells lyse at neutral pH. Research has shown that Thermoplasma volcanium may be the host cell of the endosymbrosis theory of eukaryotic cells. Hence, the genome is sequenced to confirm this hypothesis.<br />
<br />
==Genome structure==<br />
<br />
Thermoplasma volcanium has a circular DNA with 1,584,804 nucleotides. It does not contain any plasmids. However, it possesses about 70 proteins not found in any other archaea’s genome.<br />
<br />
==Cell structure and metabolism==<br />
<br />
This microbe has a unique cell membrane that contains tetraether lipids. It lacks any kind of cell wall, which causes it to have irregular shapes and is capable of assuming different shapes. The microbe uses multiple flagella for high motility. <br />
Thermoplasma volcanium is heterotrophic and therefore requires it to obtain nutrients from other organisms especially those who cannot survive in acidic or high temperature environments. Depending on its living conditions, the microbe is both anaerobic and aerobic. It is anaerobic in the presence of elemental sulfur.<br />
<br />
==Ecology==<br />
<br />
Due to its evolutionary ties to eukaryotes, Thermoplasma genus can be used as model organism for researches.<br />
<br />
==Pathology==<br />
<br />
There is no known pathogen among different strains of Thermoplasma volcanium.<br />
<br />
==Application to Biotechnology==<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=User:Landonguyen&diff=11020User:Landonguyen2007-05-24T04:43:29Z<p>Landonguyen: New page: CLASSICFICATION</p>
<hr />
<div>CLASSICFICATION</div>Landonguyenhttps://microbewiki.kenyon.edu/index.php?title=Shigella&diff=11019Shigella2007-05-24T04:21:38Z<p>Landonguyen: /* Classification */</p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
[[image:shigella_stool.jpg|right|thumb|450px|[[help:contents|Shigella bacteria in a stool sample. Image in public domain; found in Wikipedia.]]]]<br />
<br />
<br />
methyllobacillius flagellatus\<br />
<br />
==Background Information==<br />
<br />
===History===<br />
Shigella organisms are a group of gram-negative pathogens, which were initially recognized as the causal agents of shigellosis (also known as bacillary dysentery) in the 1890s. Shigella became an official genus in the 1950s, consisting of four species: ''S. dysenteriae'', ''S. flexneri'', ''S. boydii'', and ''S. sonnei''. Each of these species have their own responsibilities. ''S. dysenteriae'' serotype 1 causes deadly epidemics, ''S boydii'' is restricted to the Indian subcontinent, and ''S. flexneri'' and ''S. sonnei'' are prevalent in developing and developed countries, respectively. ''S. flexneri'', an enteroinvasive gram-negative bacterium, is responsible for the worldwide endemic form of bacillary dysentery.<br />
<br />
===Description===<br />
Shigiella is a non spore forming gram negative bacteria that aids in the facilitation of intracellular pathogens. It is able to survive the proteases and acids of the intestinal tract and infections to hosts can be caused from a very low dose. As little as 10 to 100 bacteria are needed to cause infection.<br />
<br />
==Genome structure==<br />
The four difference species of Shigella vary greatly in the genomic structure. The largest species ''S. sonnei'' contains 4,825,265 base pairs. ''S. flexneri'' contains 4,607,203 base pairs, ''S. boydii'' contains 4,519,823 base pairs and the smallest species ''S. dysenteriae'' contains 4,369,232 base pairs.<br />
<br />
==Structure and Life Functions==<br />
<br />
===Cell Structure===<br />
Shigiella is a non spore forming gram negative bacteria that aids in the facilitation of intracellular pathogens. It is able to survive the proteases and acids of the intestinal tract and infections to hosts can be caused from a very low dose. As little as 10 to 100 bacteria are needed to cause infection.<br />
<br />
===Life Cycle===<br />
The Shigella life cycle begins with penetration of colonic mucosa. This results in degradation of the epithelium and acute inflammatory<br />
colitis in the lamina propria. This causes leakage of blood, inflammation in the colon, and mucus into the intestinal lumen.<br />
<br />
[[image:shigellalifecycle.jpg|center|thumb|750px|[[help:contents|Life cycle of Shigella bacteria; courtesy of Samuel Baron, Graduate School of Biomedical Sciences at UTMB.]]]]<br />
<br />
===Metabolism===<br />
Shigella pathogens use a mixed acid fermentation pathway to metabolize substrates. Products of this anaerobic pathway include ethanol, acetic acid, lactic acid, succinic acid, formic acid, and CO2.<br />
<br />
==Pathology==<br />
<br />
===Transmission===<br />
Fecal-oral transmission is the main path of Shigellosis infection however other modes of transmission include ingestion of contaminated food or water, contact with a contaminated inanimate object, and sexual contact. Outbreaks of Shigellosis infection are common in places where sanitation is poor.<br />
<br />
===Frequency===<br />
''Shigella spp.'' Infects around 450,000 individuals just in the United States yearly, and of those 450,000 cases approximately 6,000 infected people require hospitalization to treat the aliment. Of the various strains of shigella, ''S. sonnei'' is the cause of 78% of infections, and ''S. flexneri'', and ''S. boydii'' combined are responsible for the rest of the remaining 22% of cases. The occurrence of ''S. dysenteriae'' is rare in the United States, it is however more common in developing countries with poor sanitary conditions, and water purification systems.<br />
Worldwide there are approximately 165 million cases of shigella annually, with 98% of those cases occurring in third world, developing nations. In those developing nations shigella was responsible for 1 million deaths. Unlike in the United States there are a fair amount of cases especially those resulting in death are due to the infection of ''S. dysenteriae'' it accounts for 30% of infections. Developing countries are some 20 times more likely to develop a case of shigella then more developed countries. In developed countries the number of fatal cases is around 1%, and in countries of the Far and Middle East the fatality is more along the lines of 20% of cases result in death.<br />
The majority of cases of shigella are reported in the summer months. The majority of shigella cases occur in children 15 years old and under accounting for 50% of reported cases. This is most like due to poor personal hygiene and hand washing technique, or lack there of. It is difficult to have an extremely accurate gauge of the actual number of cases that occur because 90-95% of shigella infections are typically asymptomatic so they may go unnoticed, and thus unreported.<br />
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==Current Research==<br />
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High Prevalence of Antimicrobial Resistance among Shigella Isolates in the United States Tested by the National Antimicrobial Resistance Monitoring System from 1999 to 2002, Sivapalasingam, S., Nelson, J. M., Joyce, K., Hoekstra, M., Angulo, F. J., and Mintz, E. D.<br />
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-This information on shigella's resistance to various antibiotics will help in treating shigellosis. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16377666#N0x84ceb98.0x902c5f0#N0x84ceb98.0x902c5f0 Click this hyperlink for the full text of this article.]<br />
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==References==<br />
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Hale, Thomas L. Genetic Basis of Virulence in Shigella Species. Dept. of Enteric Infections, Walter Reed Amry Institute of Research. Washington, D. C.: American Society for Microbiology, 1991. 206-224. 10 Nov. 2006 <http://mmbr.asm.org/cgi/reprint/55/2/206.pdf>. <br />
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Hale, Thomas L., and Gerald T. Keusch. "Shigella." GSBS At UTMB. The Graduate School of Biomedical Sciences at UTMB. 10 Nov. 2006 <http://www.gsbs.utmb.edu/microbook/ch022.htm>. <br />
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Sivapalasingam, S. "High Prevalence of Antimicrobial Resistance among Shigella Isolates in the United States Tested by the National Antimicrobial Resistance Monitoring System from 1999 to 2002." PubMed Central. New York, NY: NYU School of Medicine, 2006. 17 Nov. 2006 <http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16377666#N0x84ceb98.0x92357c0#N0x84ceb98.0x92357c0>.<br />
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Sureshbabu, Jaya, and Poothirikovil Venugopalan. "Shigella Infection." EMedicine From WebMD. 12 Sept. 2006. WebMD. 10 Nov. 2006 <http://www.emedicine.com/ped/topic2085.htm>.<br />
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Toebe, Carol. "Microbial Metabolism." CCSF. City College of San Francisco. 17 Nov. 2006 <http://cloud.ccsf.edu/Departments/Biology/ctoebe/metab.htm>.<br />
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Edited by Deidre DeSilva, Kayleigh Erazmus, and Megan Harney under [http://www.sacredheart.edu/pages/1274_kirk_bartholomew_ph_d_.cfm Dr. Kirk Bartholomew] of Sacred Heart University, Fairfield, CT.</div>Landonguyen