title: Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea.
abstract: Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 and ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about anaerobic methane oxidation at the molecular level, the evolutionary relationship between methane-oxidizing archaea (MOA) and methanogenic archaea raises the possibility that MOA have co-opted key elements of the methanogenic pathway, reversing many of its steps to oxidize methane anaerobically. In order to explore this hypothesis, the existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in ANME-1 and ANME-2 archaea isolated from various marine environments. Clone libraries targeting a conserved region of the alpha subunit of MCR (mcrA) were generated and compared from environmental samples, laboratory-incubated microcosms, and fosmid libraries. Four out of five novel mcrA types identified from these sources were associated with ANME-1 or ANME-2 group members. Assignment of mcrA types to specific phylogenetic groups was based on environmental clone recoveries, selective enrichment of specific MOA and mcrA types in a microcosm, phylogenetic congruence between mcrA and small-subunit rRNA tree topologies, and genomic context derived from fosmid sequences. Analysis of the ANME-1 and ANME-2 mcrA sequences suggested the potential for catalytic activity based on conservation of active-site amino acids. These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea.
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California 95039-9644, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.forename: Peter R
authors.initials: PR
authors.lastname: Girguis
authors.forename: Christina M
authors.initials: CM
authors.lastname: Preston
authors.forename: Paul M
authors.initials: PM
authors.lastname: Richardson
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D003360:Cosmids; D019641:DNA, Archaeal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D015723:Gene Library; D019766:Genes, Archaeal; D014644:Genetic Variation; D008697:Methane / Q000378:metabolism*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane