Genomic characterization of methanomicrobiales reveals three classes of methanogens.
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).
Anderson
Iain
I
Joint Genome Institute, Walnut Creek, California, USA. IJAnderson@lbl.gov
Ulrich
Luke E
LE
Lupa
Boguslaw
B
Susanti
Dwi
D
Porat
Iris
I
Hooper
Sean D
SD
Lykidis
Athanasios
A
Sieprawska-Lupa
Magdalena
M
Dharmarajan
Lakshmi
L
Goltsman
Eugene
E
Lapidus
Alla
A
Saunders
Elizabeth
E
Han
Cliff
C
Land
Miriam
M
Lucas
Susan
S
Mukhopadhyay
Biswarup
B
Whitman
William B
WB
Woese
Carl
C
Bristow
James
J
Kyrpides
Nikos
N
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
D019843:Archaeal Proteins; D012808:Sigma Factor