Methanosaeta thermophila: Difference between revisions

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<font size=14 color ="Blue">''Methanosaeta thermophila''</font>
{{Curated}}
{{Biorealm Genus}}


 
==Classification==
 
Domain: Archaea
<font size=12 color="Purple">● ~Classification~</font>
 
<font size=4 color="black">
            Organism Name: Methanosaeta thermophila PT
                    Domain: Archaea
                     Phylum: Euryarchaeota
                     Phylum: Euryarchaeota
                       Class: Methanomicrobia
                       Class: Methanomicrobia
                    Order: Methanosarcinales
                      Order: Methanosarcinales
                     Family: Methanosaetaceae
                     Family: Methanosaetaceae
                     Genus: Methanosaeta
                     Genus: Methanosaeta
Line 18: Line 14:
                                           Methanothrix thermophila DSM 6194  
                                           Methanothrix thermophila DSM 6194  
           Equivalent names:    Methanosaeta thermophila strain PT
           Equivalent names:    Methanosaeta thermophila strain PT
                                 Methanosaeta thermophila str. PT
                                 Methanosaeta thermophila strain PT


<font size=12 color="Purple">●~Description and Significance~</font>
==Description and Significance==


              
              
Line 26: Line 22:
             ''Methanosaeta thermophila'' are nonmotile, nonsporulating, and  
             ''Methanosaeta thermophila'' are nonmotile, nonsporulating, and  
   thermophilic, which means they thrive at temperatures of 50ºC or higher.
   thermophilic, which means they thrive at temperatures of 50ºC or higher.
          This microbe was discovered by a molecular technique using fluorogenic
   The addition of ''Methanosaeta'' to the methanoarchaeal genome  
   PCR polymerase chain reaction, which amplifies DNA) to identify its
  methanotrophic and activity in marine anoxic microbial communities. This was
  accomplished by identifying and quantifying the mcrA genes. Following
  amplification, molecular analysis was performed by clone analysis of the 16S
  rRNA and mcrA genes.  The mcrA genes (encoding the methyl coenzyme M reductase,
  specific to methanogenic archaea), are specific to the various phylogenetic
  groups of methanotropic Archaea. ''Methanosaeta thermophila'' was identified
  among the microbial communities in deep sediments and “methane seepages of
  Omine Ridge in the Nankai Trough accretionary prism,” (1). 
            The addition of ''Methanosaeta'' to the methanoarchaeal genome  
   sequence compilation offered an opportunity to gain significant insight into  
   sequence compilation offered an opportunity to gain significant insight into  
   this intricate microbe and the unique use of comparative genomic approaches  
   this intricate microbe and the unique use of comparative genomic approaches  
Line 44: Line 30:
   creators of biofuels (fuels derived from a biomass).
   creators of biofuels (fuels derived from a biomass).


<font size=12 color="Purple">●~Genome Structure~</font>
==Genome Structure==


            The Methanosaeta thermophila’s genome has been entirely sequenced.  These microbes  
The ''Methanosaeta thermophila'' genome has been entirely sequenced.   
possess circular chromosomes and do not contain plasmids. (The following genome sequence  
  These microbes possess circular chromosomes and do not contain plasmids.  
information, list, and map of the Methanosaeta thermophila chromosome was taken from the
  (The following genome sequence information is from reference # 11)
eleventh source listed under the references section.)
         Genome Sequence: RS: NC_008553     
         Genome Sequence: RS: NC_008553     
         Genome Sequence Length: 1879471  
         Genome Sequence Length: 1879471  
Line 55: Line 40:
                     Number of protein genes: 1696
                     Number of protein genes: 1696
                     Number of RNA genes: 51
                     Number of RNA genes: 51
          Genome Statistics                    Number % of Total
          
              DNA, total number of bases        total    100.00%
==Cell Structure and Metabolism==
              DNA G+C number of bases             0.00%
''Methanosaeta thermophila'' is circular (coccus), with one inner membrane
              DNA scaffolds                       0   100.00%
  and one cell wall. This microbe does not interact with other organisms, grows  
              Genes total number               0   100.00%
  extremely slow, does not contain plasmids, does not possess flagella, but they  
              Protein coding genes               0     0.00%
  do however produce gas vacuoles to help them move in aquatic environments. Gas
              RNA genes                               0     0.00%
  vacuoles are cavities within the cytoplasm, which contain a gas similar to that  
              rRNA genes                       0     0.00%
  of their surrounding atmosphere. These vacuoles serve as flotation devices  
              5S rRNA                               0     0.00%
  because they decrease in size when subjected to increased hydrostatic pressure.  
              16S rRNA                               0     0.00%
  So although they are nonmotile, their gas vacuoles allow some degree of  
              18S rRNA                               0     0.00%
  flexibility in regards to how much movement they have in aquatic environments.     
              23S rRNA                               0     0.00%
       ''Methanosaeta thermophila'' obtain their energy as a “thermophilic  
              28S rRNA                               0     0.00%
  obligately-aceticlastic methane-producing archaeon,” which means that they  
              tRNA genes                              0     0.00%
  produce methane from acetate (4).  Although approximately two-thirds of all  
              Other RNA genes                       0     0.00%
  methane is derived from the methyl group of acetate, ''Methanosaeta'' are able
              Genes with function prediction         0     0.00%
  to utilize acetate as a substrate for methanogenesis. ''Methanosarcina'' is  
              Genes without function prediction      0     0.00%
  the only other genus of methanoarchaea that are capable of utilizing acetate
      Genes w/o function with similarity      0     0.00%
  as a substrate, as well as using H2/CO2, dimethylsulfide, and and methanethiol  
              Genes w/o function w/o similarity      0     0.00%
  compounds as substrates.  Unlike the faster-growing ''Methanosarcina'', which  
              Pseudo Genes                       0     0.00%
  prefers methylated compounds to acetate, ''Methanosaeta'' is a slow-growing  
              Genes assigned to enzymes              0     0.00%
  specialist that utilizes acetate only.
              Genes connected to KEGG pathways       0     0.00%
              Genes not connected to KEGG pathway    0     0.00%
              Genes in ortholog clusters       0     0.00%
              Genes in paralog clusters               0     0.00%
              Genes in COGs                       0     0.00%
              Genes in Pfam                       0     0.00%
              Genes in TIGRfam                       0     0.00%
              Genes in InterPro                       0     0.00%
              Genes with IMG Terms               0     0.00%
              Genes in IMG Pathways               0     0.00%
              Obsolete Genes                       0     0.00%
              Revised Genes                       0     0.00%
              Pfam clusters               0    0.00%
              Paralogous groups               0  100.00%
              Orthologous groups       0    0.00%
 
<font size=12 color="Purple">●~Cell Structure and Metabolism~</font> 
 
      ''Methanosaeta thermophila'' is circular (coccus), with one inner membrane and one cell wall.  
This microbe does not interact with other organisms, grows extremely slow, does not contain
plasmids, does not possess flagella, but they do however produce gas vacuoles to help them move in
aquatic environments. Gas vacuoles are cavities within the cytoplasm, which contain a gas similar    
to that of their surrounding atmosphere. These vacuoles serve as floatation devices because they
decrease in size when subjected to increased hydrostatic pressure. So although they are nonmotile,  
their gas vacuoles allow some degree of flexibility in regards to how much movement they have in  
aquatic environments.     
       ''Methanosaeta thermophila'' obtain their energy as a “thermophilic obligately-aceticlastic  
methane-producing archaeon,” which means that they produce methane from acetate, (4).  Although  
approximately two-thirds of all methane is derived from the methyl group of acetate,
''Methanosaeta'' are able to utilize acetate as a substrate for methanogenesis.  
''Methanosarcina'' is the only other genus of methanoarchaea that are capable of utilizing acetate  
as a substrate, as well as using H2/CO2, dimethylsulfide, and and methanethiol compounds as  
substrates.  Unlike the faster-growing ''Methanosarcina'', which prefers methylated compounds to  
acetate, ''Methanosaeta'' is a slow-growing specialist that utilizes acetate only.


     


<font size=12 color="Purple">●~Ecology~</font>   


        The environment at which ''Methanosaeta thermophiles'' are found is aquatic (living and
==Ecology==    
growing in water) and they exhibit optimal growth between 55-60°C. Although they are present in
many environments, such as anaerobic digesters, anaerobic biofilms, sediments, and anaerobic
sludges, they are predominantly found in rice paddies, which allow a continuous stream of water to
flow through them. Acetate is the most important substrate for methanogenesis in rice paddies and
studies have shown that the concentration of acetate in flooded rice paddies is in the 5-100 mM
range, and ''Methanosaeta thermophiles'' are the predominant acetate-utilizing methanoarchaea in
these aquatic rice paddies.    
      ''Methanosaeta species are the most prevalent methanogenic archaea of the microbial
population in numerous environments, including rough sludge digesters, solid wastes, sewage slush,
and anaerobic reactors.  During activation of anaerobic bioreactors, ''Methanosaeta'' species are 
widespread due to the high acetate concentration. However, as bioreactors become stable and attain
their peak performance, the acetate concentration decreases, as well as the ''Methanosaeta'' 
population.


        The environment at which ''Methanosaeta thermophiles'' are found is
  aquatic (living and growing in water) and they exhibit optimal growth between
  55-60°C.
  ''Methanosaeta species are the most prevalent methanogenic archaea of
  the microbial population in numerous environments, including rough sludge
  digesters, solid wastes, sewage slush,and anaerobic reactors.  During activation
  of anaerobic bioreactors, ''Methanosaeta'' species are widespread due to the
  high acetate concentration. However, as bioreactors become stable and attain
  their peak performance, the acetate concentration decreases, as well as the
  ''Methanosaeta'' population.


<font size=12 color="Purple">●~Pathology~</font>
===Pathology===


         ''Methanosaeta thermofiles''are not pathogens and therefore are not disease causing  
         ''Methanosaeta thermophila''are not pathogens and therefore are not disease  
microbes. To this date, there are no known archaea that are pathogens.
  causing microbes. To this date, there are no known archaea that are pathogens.


==Current Research==


<font size=12 color="Purple">●~Application to Biotechnology~</font>  
        Although ''Methanosaeta'' continues to be comprehensively studied both
  biochemically and genetically, studies have decreased due to its slow growth
  (up to 12 days doubling time) and lower growth yield than other microbes. 
  One current study of this microbe by Alber, B.E. and Ferry J.G., determined
  that ''Methanosaeta thermophila'' archaea produce a carbonic anhydrase, which
  is an enzyme that catalyzes the reaction of water with carbon dioxide. The
  carbonic anhydrase(abbreviated CA) from acetate-grown ''Methanosaeta
  thermophila'' was purified. The molecular mass of the enzyme (CA) was
  determined via gel filtration chromatography. The results indicated that
  this particular CA represented a distinct class of CA’s and provided a
  foundation to determine the unique roles for CA in acetotrophic anaerobes.
        Another study detected central glutamates in the acetate kinase from
  the ''Methanosaeta thermophila''. Acetate kinase is an enzyme which catalyzes
  the reversible phosphorylation (adding a phosphate group) of acetate. The
  suggested mechanism denoted an unspecified glutamate residue was phosphorylated,
  and the “alignment of the amino acid sequences for the acetate kinases from
  ''E. coli'' (Bacteria domain), ''Methanosarcina thermophila'' (Archaea domain),
  and four other phylogenetically divergent microbes revealed high identity
  which included five glutamates,” (9). These glutamates were substituted in
  the ''M. thermophila'' enzyme to determine if they were required for catalysis.
  The substituted enzymes were tagged and created in ''E. coli'' and purified by
  metal affinity chromatography. The substituted enzymes produced undetectable
  kinase activity. These results imply that the glutamates in the acetate
  kinase were in fact required for catalysis, which supports the original
  suggested mechanism.


        ''Methanosaeta thermofiles are relevant for biotechnology, energy production, and as major
==References==
manufacturers as biofuels. As methanogens, ''M. thermophila'' is a source of natural gas and could
be useful producers of biofuels because they can metabolize acetate into methane by “reducing the
methyl group to CH4 with electrons derived from oxidation of the carbonyl group to CO2,” (5). With
biofuels, fuel is produced from various resources, such as plants, vegetable oils, and treated
municipal and industrial wastes. The use of biofuels as a preservative to petroleum-based fuels can
have the effect of burning with less discharge of carbon monoxide and pollutants, helping to
produce a cleaner environment.
        ''Methanosaeta thermofiles'' are also contributors to biogas. Biogas is the product of the
anaerobic breakdown of organic matter, such as sewage and waste products, by bacteria, which
produce a mixture of methane and carbon dioxide. This reaction is important because biogases are
used in the generation of hot water and electricity.


  1) Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T.,
    Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L.,
    Schmutz J.,  Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Smith K.S.,
    Ingram-Smith C., Richardson P.; "Complete sequence of Methanosaeta thermophila
    PT."; Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
  2) Identification of Essential Glutamates in the Acetate Kinase from
    Methanosarcina thermophila. Singh-Wissmann K, Ingram-Smith C, Miles RD, Ferry
    JG. J Bacteriol. 1998 Mar; 180(5): 1129-1134.
  3) Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Smith KS,
    Jakubzick C, Whittam TS, Ferry JG. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26):
    15184-15189.
  4) A carbonic anhydrase from the archaeon Methanosarcina thermophila.
    Alber BE, Ferry JG. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15): 6909-6913.
  6)  NCBI, Joint Genome Institute, Unpublished, October 25, 2006, Richardson P
      http://www.genomesonline.org/DBs/goldtable.txt
  7) http://www.genome.jp/kegg-bin/show_organism?org=mtp
  8) ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Methanosaeta_thermophila_PT/
  9) http://genome.jgi-psf.org/draft_microbes/metth/metth.info.html
10) NCBI/RefSeq:NC_008553 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val
    =NC_008553
11) Map of Chromosome: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonCircMaps&page
    =circMaps&taxon_oid=639633038&pidt=25318.1178126134
12) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html
13) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html
14) http://expasy.org/sprot/hamap/METTP.html
15) http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=349307


<font size=12 color="Purple">●~Current Research~</font>


        Although ''Methanosaeta'' continues to be comprehensively studied both biochemically and 
KMG
genetically, studies have decreased due to its slow growth (up to 12 days doubling time) and lower
growth yield than other microbes.  One current study of this microbe by Alber, B.E. and Ferry J.G.,
determined that ''Methanosaeta thermofile'' archaea produce a carbonic anhydrase, which is an
enzyme that catalyzes the reaction of water with carbon dioxide. The carbonic anhydrase
(abbreviated CA) from acetate-grown ''Methanosaeta thermophila'' was purified. The molecular mass
of the enzyme (CA) was determined via gel filtration chromatography. The results indicated that
this particular CA represented a distinct class of CA’s and provided a foundation to determine the
unique roles for CA in acetotrophic anaerobes.
        Another study detected central glutamates in the acetate kinase from the ''Methanosaeta
thermophila''. Acetate kinase is an enzyme which catalyzes the reversible phosphorylation (adding
a phosphate group) of acetate. The suggested mechanism denoted an unspecified glutamate residue was
phosphorylated, and the “alignment of the amino acid sequences for the acetate kinases from E. coli
(Bacteria domain), ''Methanosarcina thermophila'' (Archaea domain), and four other phylogenetically
divergent microbes revealed high identity which included five glutamates,” (9). These glutamates
were substituted in the ''M. thermophila'' enzyme to determine if they were required for catalysis.
The substituted enzymes were tagged and created in E. coli and purified by metal affinity
chromatography. The substituted enzymes produced undetectable kinase activity.  These results imply
that the glutamates in the acetate kinase were in fact required for catalysis, which supports the
original suggested mechanism.
        A third study explored new methods which permitted genetic analysis within the Archaea
domain. Several separately, individually, replicating plasmid shuttle vectors were constructed.
These vectors that were created were successful at replication in 9 of the 11 ''Methanosaeta''
strains tested. A method was created where DNA was brought in by liposomes, which permitted for
extremely for transformation. During the course of this study, the complete DNA sequence was
determined.

Latest revision as of 15:25, 7 July 2011

This is a curated page. Report corrections to Microbewiki.

A Microbial Biorealm page on the genus Methanosaeta thermophila

Classification

Domain: Archaea

                   Phylum:	Euryarchaeota
                     Class:	Methanomicrobia
                     Order:	Methanosarcinales
                   Family:	Methanosaetaceae
                    Genus: 	Methanosaeta
                  Species:     Methanothrix thermophila
     Genus Species Strain:     Methanosaeta thermophila PT
             Name History:	Synonyms: Methanothrix thermophila PT
                                         Methanothrix thermophila DSM 6194 
         Equivalent names:     Methanosaeta thermophila strain PT
                               Methanosaeta thermophila strain PT

Description and Significance

           Methanosaeta thermophila are nonmotile, nonsporulating, and 
 thermophilic, which means they thrive at temperatures of 50ºC or higher.
 The addition of Methanosaeta to the methanoarchaeal genome 
 sequence compilation offered an opportunity to gain significant insight into 
 this intricate microbe and the unique use of comparative genomic approaches 
 allows one to address the nature of these specific microbes and their biological 
 influence and capability. Because these microbes are methanogens, they serve 
 an important role as the producers of natural gas and have potential as 
 creators of biofuels (fuels derived from a biomass).

Genome Structure

The Methanosaeta thermophila genome has been entirely sequenced.

 These microbes possess circular chromosomes and do not contain plasmids. 
 (The following genome sequence information is from reference # 11)
        Genome Sequence: RS: NC_008553     
        Genome Sequence Length: 1879471 
        Statistics: Number of nucleotides: 1879471
                    Number of protein genes: 1696
                    Number of RNA genes: 51
        

Cell Structure and Metabolism

Methanosaeta thermophila is circular (coccus), with one inner membrane
 and one cell wall. This microbe does not interact with other organisms, grows 
 extremely slow, does not contain plasmids, does not possess flagella, but they 
 do however produce gas vacuoles to help them move in aquatic environments. Gas
 vacuoles are cavities within the cytoplasm, which contain a gas similar to that 
 of their surrounding atmosphere. These vacuoles serve as flotation devices 
 because they decrease in size when subjected to increased hydrostatic pressure. 
 So although they are nonmotile, their gas vacuoles allow some degree of 
 flexibility in regards to how much movement they have in aquatic environments.    
      Methanosaeta thermophila obtain their energy as a “thermophilic 
 obligately-aceticlastic methane-producing archaeon,” which means that they 
 produce methane from acetate (4).  Although approximately two-thirds of all 
 methane is derived from the methyl group of acetate, Methanosaeta are able
 to utilize acetate as a substrate for methanogenesis. Methanosarcina is 
 the only other genus of methanoarchaea that are capable of utilizing acetate
 as a substrate, as well as using H2/CO2, dimethylsulfide, and and methanethiol 
 compounds as substrates.  Unlike the faster-growing Methanosarcina, which 
 prefers methylated compounds to acetate, Methanosaeta is a slow-growing 
 specialist that utilizes acetate only.  



Ecology

       The environment at which Methanosaeta thermophiles are found is 
 aquatic (living and growing in water) and they exhibit optimal growth between
 55-60°C. 
 Methanosaeta species are the most prevalent methanogenic archaea of 
 the microbial population in numerous environments, including rough sludge 
 digesters, solid wastes, sewage slush,and anaerobic reactors.  During activation 
 of anaerobic bioreactors, Methanosaeta species are widespread due to the 
 high acetate concentration. However, as bioreactors become stable and attain 
 their peak performance, the acetate concentration decreases, as well as the 
 Methanosaeta population.

Pathology

       Methanosaeta thermophilaare not pathogens and therefore are not disease 
 causing microbes. To this date, there are no known archaea that are pathogens.

Current Research

        Although Methanosaeta continues to be comprehensively studied both
 biochemically and genetically, studies have decreased due to its slow growth
 (up to 12 days doubling time) and lower growth yield than other microbes.  
 One current study of this microbe by Alber, B.E. and Ferry J.G., determined 
 that Methanosaeta thermophila archaea produce a carbonic anhydrase, which 
 is an enzyme that catalyzes the reaction of water with carbon dioxide. The 
 carbonic anhydrase(abbreviated CA) from acetate-grown Methanosaeta 
 thermophila was purified. The molecular mass of the enzyme (CA) was 
 determined via gel filtration chromatography. The results indicated that 
 this particular CA represented a distinct class of CA’s and provided a 
 foundation to determine the unique roles for CA in acetotrophic anaerobes.
        Another study detected central glutamates in the acetate kinase from 
 the Methanosaeta thermophila. Acetate kinase is an enzyme which catalyzes
 the reversible phosphorylation (adding a phosphate group) of acetate. The
 suggested mechanism denoted an unspecified glutamate residue was phosphorylated, 
 and the “alignment of the amino acid sequences for the acetate kinases from 
 E. coli (Bacteria domain), Methanosarcina thermophila (Archaea domain), 
 and four other phylogenetically divergent microbes revealed high identity 
 which included five glutamates,” (9). These glutamates were substituted in
 the M. thermophila enzyme to determine if they were required for catalysis. 
 The substituted enzymes were tagged and created in E. coli and purified by 
 metal affinity chromatography. The substituted enzymes produced undetectable 
 kinase activity.  These results imply that the glutamates in the acetate
 kinase were in fact required for catalysis, which supports the original 
 suggested mechanism.

References

 1) Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T.,
    Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L.,
    Schmutz J.,  Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Smith K.S., 
    Ingram-Smith C., Richardson P.; "Complete sequence of Methanosaeta thermophila 
    PT."; Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
 2) Identification of Essential Glutamates in the Acetate Kinase from 
    Methanosarcina thermophila. Singh-Wissmann K, Ingram-Smith C, Miles RD, Ferry
    JG. J Bacteriol. 1998 Mar; 180(5): 1129-1134.
 3) Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Smith KS,
    Jakubzick C, Whittam TS, Ferry JG. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26): 
    15184-15189.
 4) A carbonic anhydrase from the archaeon Methanosarcina thermophila.
    Alber BE, Ferry JG. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15): 6909-6913.
 6)  NCBI, Joint Genome Institute, Unpublished, October 25, 2006, Richardson P 
     http://www.genomesonline.org/DBs/goldtable.txt
 7) http://www.genome.jp/kegg-bin/show_organism?org=mtp
 8) ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Methanosaeta_thermophila_PT/
 9) http://genome.jgi-psf.org/draft_microbes/metth/metth.info.html
10) NCBI/RefSeq:NC_008553 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val
    =NC_008553
11) Map of Chromosome: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonCircMaps&page
    =circMaps&taxon_oid=639633038&pidt=25318.1178126134
12) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html
13) http://genome.jgi-psf.org/finished_microbes/metth/metth.home.html 
14) http://expasy.org/sprot/hamap/METTP.html
15) http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=349307


KMG