title: Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.
abstract: We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.
authors.affiliation: Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan. sakai-s@jamstec.go.jp
authors.forename: Sanae
authors.initials: S
authors.lastname: Sakai
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Takaki
authors.forename: Shigeru
authors.initials: S
authors.lastname: Shimamura
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
authors.forename: Takahisa
authors.initials: T
authors.lastname: Tajima
authors.forename: Hiroki
authors.initials: H
authors.lastname: Kosugi
authors.forename: Natsuko
authors.initials: N
authors.lastname: Ichikawa
authors.forename: Eiji
authors.initials: E
authors.lastname: Tasumi
authors.forename: Aiko T
authors.initials: AT
authors.lastname: Hiraki
authors.forename: Ai
authors.initials: A
authors.lastname: Shimizu
authors.forename: Yumiko
authors.initials: Y
authors.lastname: Kato
authors.forename: Rika
authors.initials: R
authors.lastname: Nishiko
authors.forename: Koji
authors.initials: K
authors.lastname: Mori
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Fujita
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Imachi
authors.forename: Ken
authors.initials: K
authors.lastname: Takai
mesh_terms: D000085:Acetates / Q000378:metabolism; D001639:Bicarbonates / Q000378:metabolism; D002250:Carbon Radioisotopes; D002874:Chromosome Mapping; D019641:DNA, Archaeal / Q000032:analysis*; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D018698:Glutamic Acid / Q000378:metabolism; D008697:Methane / Q000378:metabolism*; D017018:Methanomicrobiales / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D000085:Acetates; D001639:Bicarbonates; D002250:Carbon Radioisotopes; D019641:DNA, Archaeal; D018698:Glutamic Acid; D008697:Methane