A 6-kilobase-pair (kbp) region of the genome of the extremely thermophilic archaebacterium Methanothermusfervidus which encodes the a, ,1, and y subunit polypeptides of component C of methyl coenzyme M reductase was cloned and sequenced. Genes encoding the (mcrB) and -y (merG) subunits were separated by two open reading frames (designated mcrC and mcrD) which encode unknown gene products. The M. fervidus genes were preceded by ribosome-binding sites, separated by short A+T-rich intergenic regions, contained unexpectedly few NNC codons, and exhibited inflexible codon usage at some locations. Sites of transcription initiation and termination flanking the mcrBDCGA cluster of genes in M. fervidus were identified. The sequences of the genes, the encoded polypeptides, and transcription regulatory signals in M. fervidus were compared with the functionally equivalent sequences from two mesophilic methanogens (Methanococcus vannielii and Methanosarcina barkeri) and from a moderate thermophile (Methanobacterium thermoautotrophicum Marburg). The amino acid sequences of the polypeptides encoded by the mcrBCGA genes in the two thermophiles were approximately 80% identical, whereas all other pairs of these gene products contained between 50 and 60% identical amino acid residues. The mcrD gene products have diverged more than the products of the other mcr genes. Identification of highly conserved regions within mcrA and mcrB suggested oligonucleotide sequences which might be developed as hybridization probes which could be used for identifying and quantifying all methanogens.Methanogens constitute an extremely diverse group of archaebacteria with genomes which range from 28 to 61 mol% G+C. There are bacillary, coccal, and spiral methanogens, and their habitats are as different as the human gut and volcanic vents. Their ability to synthesize methane is, however, a unifying feature, and the terminal reaction in methanogenesis, reduction of a methyl group bound to coenzyme M, is common to all methanogens (2, 12, 33). The enzyme which catalyzes this reaction, component C of methyl coenzyme M reductase (methyl reductase), has been purified from several methanogens and found in all cases to contain three different subunit polypeptides, designated ox, 1, and -y (8,11,14,18). Conservation in the structure and function of methyl reductases has been shown by immunological cross-reactivities and methanogenesis in vitro with reaction mixtures containing components prepared from different methanogens (11). Cloning and sequencing of the genes encoding the ox, 1, and -y subunits of methyl-coenzyme M reductase (mcrA, mcrB, and mcrG, respectively) from Methanococcus vannielii, Methanosarcina barkeri, and Methanobacterium thermoautotrophicum has recently been reported (4-6), and we have now extended this work to Methanothermus fervidus, a very unusual methanogen, isolated from a volcanic hot spring, with an optimum growth temperature of 83°C (25 ously reported from the two mesophiles (M. vannielii and M. barkeri) and the moderate thermophile (M...