Methanosaeta thermophila

Methanosaeta thermophila

● ~Classification~ Organism Name: Methanosaeta thermophila PT 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 str. PT

●~Description and Significance~

           Methanosaeta thermophila are a diverse group of widely distributed anaerobic archaea that occur in anaerobic environments, such as the intestinal tracts of animals, freshwater and marine sediments, sewage, anaerobic biofilms, and anaerobic sediments, and are methanogens, which means they are capable of producing methane from a limited number of substrates, including carbon dioxide and hydrogen, acetate, and methylamines. Methanosaeta thermophila are nonmotile, nonsporulating, and thermophilic, which means they thrive at temperatures of 50ºC or higher.

This microbe was discovered by a molecular technique using fluorogenic PCR to identify methanotrophic components and activity in marine anoxic microbial communities by identifying and quantifying the mcrA genes. Molecular analysis was performed by amplification and clone analysis of 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 cold deep sediments and methane seepages of Omine Ridge in the Nankai Trough accretionary prism. The addition of Methanosaeta to the methanoarchaeal genome sequence compilation offers an opportunity to gain significant insight into this difficult microbe and the unprecedented use of comparative genomic approaches allows one to address the nature of these microbes and their biological impact and potential. Because they are methanogens, they are an important source of natural gas and have potential as a producer of biofuels.

● ~Genome Structure~

The Methanosaeta thermophila’s genome has been entirely sequenced. These microbes possess circular chromosomes and do not contain plasmids. (The following Genome Statistics list was retrieved from seventh source under references.)

Genome Sequence: RS: NC_008553 Genome Sequence Length: 1879471 Statistics: Number of nucleotides: 1879471

           Number of protein genes: 1696
           Number of RNA genes: 51

Genome Statistics Number  % of Total

       DNA, total number of bases		         100.00%
       DNA coding number of bases		
       DNA G+C number of bases		                   0.00% 
       	        	        

DNA scaffolds 0 100.00%

Genes total number 0 100.00%

       Protein coding genes	             0	           0.00%
       RNA genes	                     0	           0.00%
               rRNA genes	             0	           0.00%
                       5S rRNA              0	           0.00%
                       16S rRNA	     0	           0.00%
                       18S rRNA	     0	           0.00%
                       23S rRNA	     0	           0.00%
                       28S rRNA	     0	           0.00%
               tRNA genes	             0	           0.00%
               Other RNA genes	             0	           0.00%
       Genes with function prediction	     0	           0.00%
       Genes without function prediction    0	           0.00%

       Genes w/o function with similarity   0	           0.00%
       Genes w/o function w/o similarity    0	           0.00%
       Pseudo Genes	                     0	           0.00%
       Genes assigned to enzymes	     0	           0.00%
       Genes connected to KEGG pathways     0	           0.00%
       Genes not connected to KEGG pathways 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 100.00% Orthologous groups 0.00%

Map of chromosome

Map of Methanosaeta thermophila PT: NC_008553 Legend: From outside to the center Genes on forward strand (color by COG categories) Genes on reverse strand (color by COG categories) RNA genes (tRNAs green, sRNAs red) GC content GC skew

COG Coloring Selection Color code of function category for top COG is shown below. COG Code COG Function Definition [A] RNA processing and modification [B] Chromatin structure and dynamics [C] Energy production and conversion [D] Cell cycle control, cell division, chromosome partitioning [E] Amino acid transport and metabolism [F] Nucleotide transport and metabolism [G] Carbohydrate transport and metabolism [H] Coenzyme transport and metabolism [I] Lipid transport and metabolism [J] Translation, ribosomal structure and biogenesis [K] Transcription [L] Replication, recombination and repair [M] Cell wall/membrane/envelope biogenesis [N] Cell motility [O] Posttranslational modification, protein turnover, chaperones [P] Inorganic ion transport and metabolism [Q] Secondary metabolites biosynthesis, transport and catabolism [R] General function prediction only [S] Function unknown [T] Signal transduction mechanisms [U] Intracellular trafficking, secretion, and vesicular transport [V] Defense mechanisms [W] Extracellular structures [Y] Nuclear structure [Z] Cytoskeleton NA Not assigned

● ~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 gas similar to that of their surrounding atmosphere. These vacuoles serve as floating devices because they decrease in size when subjected to increased hydrostatic pressure.       

Methanosaeta thermophila obtain their energy production as a thermophilic obligately-aceticlastic methane-producing archaeon, which means that they produce methane from acetate. Although approximately two-thirds of all biogenic methane is derived from the methyl group of acetate, Methanosaeta is one of only two genera of the methanoarchaea able to utilize acetate as a substrate for methanogenesis. Methanosarcina, the only other genus of methanoarchaea able to utilize acetate, can use H2/CO2, dimethylsulfide, and methanethiol as well as methylated C1 compounds as substrates. Unlike the faster-growing Methanosarcina, which prefers methylated compounds to acetate, Methanosaeta is a specialist that utilizes only acetate.

● ~Ecology~

The environment at which Methanosaeta thermophiles are found is aquatic 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. 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 are the predominant acetate-utilizing methanoarchaea in flooded rice paddies. Methanosaeta species also dominate the methanogenic population of microbial consortia in granular sludge digestors, codigestors treating municipal solid waste and sewage sludge, upflow anaerobic sludge blanket reactors, and anaerobic baffled reactors. During start-up of anaerobic bioreactors, Methanosarcina species are often prevalent due to the high acetate concentration; however, as bioreactors stabilize and achieve optimum performance the acetate concentration decreases and Methanosaeta species replace Methanosarcina .

● ~Pathology~

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

● ~Application to Biotechnology~

Methanosaeta thermofiles are relevant for biotechnology, energy production, and as major producers as biofuels. M. thermophila is a source of natural gas as methanogens 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. With biofuels, fuel is produced from renewable resources, such as plant biomass, vegetable oils, and treated municipal and industrial wastes. The use of biofuels as an additive to petroleum-based fuels can result in cleaner burning with less emission of carbon monoxide and particulates. Methanosaeta thermofiles are also contributors to biogas; a mixture of methane and carbon dioxide produced by the anaerobic decomposition of organic matter such as sewage and municipal wastes by bacteria. This is important because it is used in the generation of hot water and electricity.

● ~Current Research~

Although Methanosarcina continues to be extensively studied both biochemically and genetically, studies on Methanosaeta have lapsed due to its slow growth (2-12 day doubling time) and lower growth yield. One current study of this microbe by Alber, BE and Ferry JG, determined that Methanosaeta thermofile produce a carbonic anhydrase. The carbonic anhydrase (CA) from acetate-grown Methanosarcina thermophila was purified. The molecular mass of the enzyme was determined via gel filtration chromatography. The results indicate that this archaeal CA represents a distinct class of CAs and provide a basis to determine physiological roles for CA in acetotrophic anaerobes. Another study identified essential glutamates in the acetate kinase from the Methanosaeta thermophila. Acetate kinase catalyzes the reversible phosphorylation of acetate. The proposed mechanism indicated an unspecified glutamate residue was phosphorylated. 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. These glutamates were replaced in the M. thermophila enzyme to determine if any were essential for catalysis. The altered enzymes were tagged and produced in E. coli and purified by metal affinity chromatography. The enzymes showed either undetectable or extremely low kinase activity, suggesting that the glutamates in the acetate kinase were essential for catalysis, which supports the proposed mechanism. A third study titled, “A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors,” explored new methods that allow genetic analysis in Archaea. Several autonomously replicating plasmid shuttle vectors were constructed. These vectors replicate in 9 of 11 Methanosarcina strains tested and in Escherichia coli. A transformation system was established where DNA was introduced by liposomes, which allowed for extremely efficient transformation frequencies During the course of this work, the complete DNA sequence was determined.

● ~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. 5) A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors. Metcalf WW, Zhang JK, Apolinario E, Sowers KR, Wolfe RS. Proc Natl Acad Sci U S A. 1997 Mar 18; 94(6): 2626-2631. PMCID: 20139 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