title: Genomic characterization of methanomicrobiales reveals three classes of methanogens.
abstract: BACKGROUND
  Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.
  
  
  RESULTS
  In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales.
  
  
  CONCLUSIONS
  Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).
authors.affiliation: Joint Genome Institute, Walnut Creek, California, USA. IJAnderson@lbl.gov
authors.forename: Iain
authors.initials: I
authors.lastname: Anderson
authors.forename: Luke E
authors.initials: LE
authors.lastname: Ulrich
authors.forename: Boguslaw
authors.initials: B
authors.lastname: Lupa
authors.forename: Dwi
authors.initials: D
authors.lastname: Susanti
authors.forename: Iris
authors.initials: I
authors.lastname: Porat
authors.forename: Sean D
authors.initials: SD
authors.lastname: Hooper
authors.forename: Athanasios
authors.initials: A
authors.lastname: Lykidis
authors.forename: Magdalena
authors.initials: M
authors.lastname: Sieprawska-Lupa
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Dharmarajan
authors.forename: Eugene
authors.initials: E
authors.lastname: Goltsman
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Saunders
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Biswarup
authors.initials: B
authors.lastname: Mukhopadhyay
authors.forename: William B
authors.initials: WB
authors.lastname: Whitman
authors.forename: Carl
authors.initials: C
authors.lastname: Woese
authors.forename: James
authors.initials: J
authors.lastname: Bristow
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
mesh_terms: D001105:Archaea / Q000378:metabolism; D019843:Archaeal Proteins / Q000378:metabolism; D002965:Classification; D016000:Cluster Analysis; D005821:Genetic Techniques; D020745:Genome, Archaeal; D023281:Genomics; D017018:Methanomicrobiales / Q000145:classification / Q000235:genetics*; D008954:Models, Biological; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D012808:Sigma Factor