Difference between revisions of "Methanosphaera stadtmanae"

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{{Biorealm Genus}}
 
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Kingdom: Biota
 
Domain: Archaea
 
Phylum: Euryarchaeota
 
Class: Methanobacteria
 
Order: Methanobacteriales
 
Family: Methanobacteriaceae
 
 
Genus: Methanosphaera
 
Genus: Methanosphaera
 
Species: stadtmanae
 
Species: stadtmanae
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'''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]'''
 
'''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]'''
 
|}
 
|}
 
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==Description and Significance==
==Description and significance==
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The ''Methanosphaera stadtmanae strain DSZM 3091'' was isolated by the Deutsche Sammlung von Zellkulturen und Mikroorganismen (DSMZ), located in Braunschweig, Germany. It is important to isolate and sequence the genome of this archaeon as it is the first human archaeal commensal; therefore, it can help researchers gain a better understanding of the role of archael commensals in humans.   It was found that ''M. stadtmanae'' inhabits the human intestine. These archaea thrive there because methanol is present as a by product of “pectin degradation by Bacteroides species and other anaerobic bacteria”
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.
+
It was found that the ''M. stadtmanae'' can be grown on a medium that contains 0.5 g/liter sodium formate and 10% rumen fluid. The process of sequencing ''M. stadtmanae'' included extracting and shearing “its total genomic DNA to obtain various shotgun data using 3 kb to 5 kb fractions.”  Next, the fragments were cloned into vectors produced by the Invitrogen Co., pCR4-TOPO. Then, the ends of the recombinant plasmids were sequenced using dye terminator chemistry. Also, in order to edit the sequence, part of the Staden software package, GAP4, was used. In fact, about 8.7-fold coverage of the genome was achieved after reconstructing 21,555 sequences.
Include a picture or two (with sources) if you can find them.
 
 
 
 
 
''Bacillus licheniformis'' is a bacterium that is commonly found in soil and bird feathers. Birds that tend to stay on the ground more than the air (i.e. sparrows) and on the water (i.e. ducks) are common carriers of this bacterium; it is mostly found around the bird's chest area and back plumage.
 
 
 
''Bacillus licheniformis'' is part of the subtilis group along with ''Bacillus subtilis'' and ''Bacillus pumilus''. These bacteria are commonly known to cause food poisoning and food spoilage. ''Bacillus licheniformis'' also is known for contaminating dairy products. Food borne outbreaks usually involve cases of cooked meats and vegetables, raw milk, and industrially produced baby food contaminated with ''Bacillus licheniformis''.
 
  
 
==Genome structure==
 
==Genome structure==
Describe the size and content of the genomeHow many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence?
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The ''M. stadtmanae'' genome consists of one circular chromosome that contains 1,767,403 basepairs but no plasmids.  Also, of all sequenced archaeal genomes, ''M. stadtmanae'' has the lowest Guanine+Cytosine (G+C) content at 28%.  Also, within all the methanogens, the ''M. stadtmanae'' has the lowest number of protein-encoding sequences with 1,534 CDSIt is found that the ''M. stadtmanae''’s genome has 40 tRNAs and four rRNA operons, which is the highest number of rRNA operons found in a single genome within the Archaea domain. In fact, “its genome consists of four 1,528-bp insertion elements, which all include either one of three highly homologous CDS, Msp0017, Msp0233, and Msp0471, or a pseudogene, Msp1439.
Does it have any plasmids?  Are they important to the organism's lifestyle?
 
 
 
''Bacillus Licheniformis'' is a Gram positive, thermophillic bacterium. Its optimal growth temperature is 50°C, but it can also survive at much higher temperatures. Its optimal temperature for
 
  
 
==Cell structure and metabolism==
 
==Cell structure and metabolism==
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.
+
''M. stadtmanae'' needs acetate for growth.  This is because the ''M. stadtmanae'' lacks the carbon monoxide dehydrogenase and acetyl-coenzyme A synthase that is responsible for synthesizing the acetyl-coenzyme that is needed in the Krebs cycle to produce ATP, which is essential for cell growth. In addition, as demonstrated by Gerhard Gottschalk et al., the sequenced genome of ''M. stadtmanae''’s  is found to also lack “37 protein-coding sequences present in all other methanogens, which are involved in synthesis of a compound required for catalyzing the first step of methanogenesis from CO2 and H2.” For that reason, ''M. stadtmanae'' lacks the ability to perform methanogenesis and is unable to produce methane like other methanogens. Therefore, as an alternative, ''M. stadtmanae''’s genome has a protein-encoding sequences (CDS) for the enzymes that aid in the reduction of methane and ATP synthesis.  As it turned out, this is a very efficient process in terms of conserving energy for the ''M. stadtmanae'' because they only have five enzyme complexes that are involved in “methanol reduction to methane with H2, a reaction that is coupled to the buildup of an electrochemical proton potential which drives the phosphorylation of ADP,” which is found when analyzing the growth of the methanogen on H2 and methanol as the only energy source. Equally interesting, it is found that there were 3,300 amino acids sequenced in the genome of ''M. stadtmanae'' that are not present in any other methanogens or Archaea. It is believed that these amino acids have attachment features that allow ''M. stadtmanae'' to colonize in the human intestine.
 
 
==Ecology==
 
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
 
  
 
==Pathology==
 
==Pathology==
How does this organism cause disease? Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.
+
''Methanosphaera stadtmanae'' is an organism that lives in the human intestine.  ''M. stadtmanae'' is found to have the most restricted energy metabolism present in methanogenic Archaea. ''M. stadtmanae'' is restricted to methanol and H2 for methane formation and ATP synthesis as mentioned earlier.  In fact, ''M. stadtmanae'' can “neither oxidize methanol to CO2 nor reduce CO2 to methane,” which also makes this bacteria lack the ability of autotrophic growth on CO2, making them dependent on acetate and CO2 as the main carbon sources that is needed for the biosynthesis of necessary cell components.  Therefore, with this incompetent, it makes them helpful for their human host by conserving energy; this is the reason why the human intestine does not need much energy to make methane for producing essential cell components, which makes this organism a useful organism rather than a parasite. Also, unlike other commensals, ''M. stadtmanae'' are “able to survive in the human gastrointestinal tract, which is protected by a highly active immune system, but also stimulate the development of a healthy intestinal epithelium and immune system;” and therefore, can help prevent chronic inflammatory diseases of the intestine, but their specific role is still unknown to researchers.
  
 
==Application to Biotechnology==
 
==Application to Biotechnology==
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
+
''M. stadtmanae'' does produce some useful compounds such as molybdopterin, which helps the organism be able to grow without being dependent on acetate to biosynthesize cell components.  This organism also produces serine from the pyruvate that was synthesized from glycolysis(2).  Being able to produce serine is useful since it is a good carbon source and is one of the most common amino acids found in animal proteins.  Also, like all other methanogens, ''M. stadtmanae'' has the ability to synthesize the coenzyme F430, which is found to be useful in redox reactions. By producing and using the F430, which has a low energy conformation, ''M. stadtmanae'' is able to conserve energy in redox reactions. More specifically, the F430 can be used as a catalyst for the reductive dehalogenation of chlorinated carbon one hydrocarbons(1).
  
 
==Current Research==
 
==Current Research==
  
Enter summaries of the most recent research here--at least three required
+
1. “The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis”[1](2005)
 +
This current research was an attempt to find some general features about the ''M. stadtmanae'' and understand how it behaves as it inhabits in the human intestine.  It was found that while living in the human intestine, ''M. stadtmanae'' was able to generate methane by reduction of methanol with hydrogen gas.
  
 
==References==
 
==References==
[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.]
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[1] Wolfgang F. Fricke, Henning Seedorf, Anke Henne, Markus Krüer,Heiko Liesegang, Reiner Hedderich, Gerhard Gottschalk, and Rudolf K. Thauer. “The Genome Sequence of Methanosphaera stadmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis”. Journal of Bacteriology. January 2006. Volume 188. p. 642-658.
 +
 
 +
[2] Gerhard Dongowski, Angelika Lorenz, and Horst Anger. “Degradation of Pectins with Different Degrees of Esterification by Bacteroides thetaiotaomicron Isolated from Human gut Flora”. Applied and Environmental Microbiology. April 2000. Volume 66. p. 1321-1327.
 +
 
 +
[3] Marc F Whitford, Ronald M Teather, and Robert J Forster. “Phylogenetic analysis of methanogens from the bovine rumen”. BMC Microbiology. 2001. Volume 1. Open access online journal article. < http://www.biomedcentral.com/1471-2180/1/5>.
 +
 +
[4] Lovley RD, Greening RC, Ferry JG: “Rapidly Growing Rumen Methanogenic Organisms That Synthesizes Cooenzyme M and Has a High Affinity for Formate”.
 +
Applied Environmental Microbiology. 1984. Volume 48. p.81-87.
  
Edited by student of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
+
KMG

Latest revision as of 18:52, 19 August 2010

This student page has not been curated.

A Microbial Biorealm page on the genus Methanosphaera stadtmanae

Classification

Higher order taxa

Kingdom: Biota Domain: Archaea Phylum: Euryarchaeota Class: Methanobacteria Order: Methanobacteriales Family: Methanobacteriaceae

Genus

Genus: Methanosphaera Species: stadtmanae


NCBI: Taxonomy

Description and Significance

The Methanosphaera stadtmanae strain DSZM 3091 was isolated by the Deutsche Sammlung von Zellkulturen und Mikroorganismen (DSMZ), located in Braunschweig, Germany. It is important to isolate and sequence the genome of this archaeon as it is the first human archaeal commensal; therefore, it can help researchers gain a better understanding of the role of archael commensals in humans. It was found that M. stadtmanae inhabits the human intestine. These archaea thrive there because methanol is present as a by product of “pectin degradation by Bacteroides species and other anaerobic bacteria” It was found that the M. stadtmanae can be grown on a medium that contains 0.5 g/liter sodium formate and 10% rumen fluid. The process of sequencing M. stadtmanae included extracting and shearing “its total genomic DNA to obtain various shotgun data using 3 kb to 5 kb fractions.” Next, the fragments were cloned into vectors produced by the Invitrogen Co., pCR4-TOPO. Then, the ends of the recombinant plasmids were sequenced using dye terminator chemistry. Also, in order to edit the sequence, part of the Staden software package, GAP4, was used. In fact, about 8.7-fold coverage of the genome was achieved after reconstructing 21,555 sequences.

Genome structure

The M. stadtmanae genome consists of one circular chromosome that contains 1,767,403 basepairs but no plasmids. Also, of all sequenced archaeal genomes, M. stadtmanae has the lowest Guanine+Cytosine (G+C) content at 28%. Also, within all the methanogens, the M. stadtmanae has the lowest number of protein-encoding sequences with 1,534 CDS. It is found that the M. stadtmanae’s genome has 40 tRNAs and four rRNA operons, which is the highest number of rRNA operons found in a single genome within the Archaea domain. In fact, “its genome consists of four 1,528-bp insertion elements, which all include either one of three highly homologous CDS, Msp0017, Msp0233, and Msp0471, or a pseudogene, Msp1439.”

Cell structure and metabolism

M. stadtmanae needs acetate for growth. This is because the M. stadtmanae lacks the carbon monoxide dehydrogenase and acetyl-coenzyme A synthase that is responsible for synthesizing the acetyl-coenzyme that is needed in the Krebs cycle to produce ATP, which is essential for cell growth. In addition, as demonstrated by Gerhard Gottschalk et al., the sequenced genome of M. stadtmanae’s is found to also lack “37 protein-coding sequences present in all other methanogens, which are involved in synthesis of a compound required for catalyzing the first step of methanogenesis from CO2 and H2.” For that reason, M. stadtmanae lacks the ability to perform methanogenesis and is unable to produce methane like other methanogens. Therefore, as an alternative, M. stadtmanae’s genome has a protein-encoding sequences (CDS) for the enzymes that aid in the reduction of methane and ATP synthesis. As it turned out, this is a very efficient process in terms of conserving energy for the M. stadtmanae because they only have five enzyme complexes that are involved in “methanol reduction to methane with H2, a reaction that is coupled to the buildup of an electrochemical proton potential which drives the phosphorylation of ADP,” which is found when analyzing the growth of the methanogen on H2 and methanol as the only energy source. Equally interesting, it is found that there were 3,300 amino acids sequenced in the genome of M. stadtmanae that are not present in any other methanogens or Archaea. It is believed that these amino acids have attachment features that allow M. stadtmanae to colonize in the human intestine.

Pathology

Methanosphaera stadtmanae is an organism that lives in the human intestine. M. stadtmanae is found to have the most restricted energy metabolism present in methanogenic Archaea. M. stadtmanae is restricted to methanol and H2 for methane formation and ATP synthesis as mentioned earlier. In fact, M. stadtmanae can “neither oxidize methanol to CO2 nor reduce CO2 to methane,” which also makes this bacteria lack the ability of autotrophic growth on CO2, making them dependent on acetate and CO2 as the main carbon sources that is needed for the biosynthesis of necessary cell components. Therefore, with this incompetent, it makes them helpful for their human host by conserving energy; this is the reason why the human intestine does not need much energy to make methane for producing essential cell components, which makes this organism a useful organism rather than a parasite. Also, unlike other commensals, M. stadtmanae are “able to survive in the human gastrointestinal tract, which is protected by a highly active immune system, but also stimulate the development of a healthy intestinal epithelium and immune system;” and therefore, can help prevent chronic inflammatory diseases of the intestine, but their specific role is still unknown to researchers.

Application to Biotechnology

M. stadtmanae does produce some useful compounds such as molybdopterin, which helps the organism be able to grow without being dependent on acetate to biosynthesize cell components. This organism also produces serine from the pyruvate that was synthesized from glycolysis(2). Being able to produce serine is useful since it is a good carbon source and is one of the most common amino acids found in animal proteins. Also, like all other methanogens, M. stadtmanae has the ability to synthesize the coenzyme F430, which is found to be useful in redox reactions. By producing and using the F430, which has a low energy conformation, M. stadtmanae is able to conserve energy in redox reactions. More specifically, the F430 can be used as a catalyst for the reductive dehalogenation of chlorinated carbon one hydrocarbons(1).

Current Research

1. “The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis”[1](2005) This current research was an attempt to find some general features about the M. stadtmanae and understand how it behaves as it inhabits in the human intestine. It was found that while living in the human intestine, M. stadtmanae was able to generate methane by reduction of methanol with hydrogen gas.

References

[1] Wolfgang F. Fricke, Henning Seedorf, Anke Henne, Markus Krüer,Heiko Liesegang, Reiner Hedderich, Gerhard Gottschalk, and Rudolf K. Thauer. “The Genome Sequence of Methanosphaera stadmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis”. Journal of Bacteriology. January 2006. Volume 188. p. 642-658.

[2] Gerhard Dongowski, Angelika Lorenz, and Horst Anger. “Degradation of Pectins with Different Degrees of Esterification by Bacteroides thetaiotaomicron Isolated from Human gut Flora”. Applied and Environmental Microbiology. April 2000. Volume 66. p. 1321-1327.

[3] Marc F Whitford, Ronald M Teather, and Robert J Forster. “Phylogenetic analysis of methanogens from the bovine rumen”. BMC Microbiology. 2001. Volume 1. Open access online journal article. < http://www.biomedcentral.com/1471-2180/1/5>.

[4] Lovley RD, Greening RC, Ferry JG: “Rapidly Growing Rumen Methanogenic Organisms That Synthesizes Cooenzyme M and Has a High Affinity for Formate”. Applied Environmental Microbiology. 1984. Volume 48. p.81-87.

KMG