The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H ₂ for Methane Formation and ATP Synthesis

Abstract

Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H 2 and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G؉C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetylcoenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO 2 to methane or oxidize methanol to CO 2 and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventythree of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.There are two types of methanogenic archaea, those belonging to the order Methanosarcinales, which contain cytochromes and which can use methanol, methyl amines, acetate, and/or CO 2 plus H 2 as methanogenic substrates, and those belonging to the orders Methanobacteriales, Methanomicrobiales, Methanococcales, and Methanopyrales, which are devoid of cytochromes and which can use CO 2 plus H 2 and/or formate only to fuel anaerobic growth (95, 102). The energy metabolism of both types of methanogens has been investigated in detail (17). However, there are still a few pertinent questions. For example, why is the growth yield on H 2 and CO 2 of methanogens lacking cytochromes considerably lower (Ͻ50%) than that of cytochrome-containing methanogens? The growth yield on H 2 and CO 2 of Methanobrevibacter arboriphilus is 1.3 g/mol methane, whereas that of Methanosarcina barkeri is 7.3 g/mol (101). Could the reason for this be that in cytochrome-containing methanogens two steps in the reduction of CO 2 to methane, methyl transfer from methyl-tetrahydromethanopterin (methyl-H 4 MPT) to coenzyme M and reduction of the heterodisulfide coenzyme M-S-S-coenzyme B (CoM-S-S-CoB) with H 2 , are coupled with energy conservation, whereas in methanogens without cytochromes only one step, the methyltransfer reaction, is coupled? Indeed, methanogens with cytochromes contain a heterodisulfide reductase (HdrDE) that is anchored via a cytoc...

Diversity of methanogens in ruminants in Queensland

“…The dominance of Methanobrevibacter in the rumen of domestic ruminants is in accord with other recent studies in Western Australia and Canada (Wright et al 2004 but contrasts with the only other report from Queensland (Wright et al 2006), where Methanobrevibacter sequences accounted for 9% of total clones sequenced from the ruminal contents of adult sheep. From the samples examined in the present study, the only anomalies to the finding of Wright et al (2006) were the sequences from the leucaena-fed fermentor where both sequences were most closely related to the human intestinal methanogen, Methanosphaera stadtmanae (Fricke et al 2006). Sequences related to this species have also been identified previously from cattle, particularly in Canada (Whitford et al 2001;Wright et al 2007).…”

“…Sequences related to this species have also been identified previously from cattle, particularly in Canada (Whitford et al 2001;Wright et al 2007). Interestingly, M. stadtmanae is incapable of growth (and methane production) solely from carbon dioxide and hydrogen, using the methanol released during the fermentation of pectins as its primary carbon source for growth (Fricke et al 2006). Whether these 'unusual' methanogens identified from the fermentors share similar characteristics remains to be determined.…”

Diversity of gut methanogens in herbivorous animals

“…Because M. stadtmanae is unable to use hydrogen and carbon dioxide for methane synthesis and have a limited substrate range (Fricke et al, 2006), M. stadtmanaerelated methanogens are typically only found at a low prevalence in the gut of herbivores. It has been hypothesized that perhaps the degradation of large amounts of fruit pectin in frugivore hosts such as the orangutan may result in increased levels of methanol and acetate, which would favor the growth of M. stadtmanae methanogens (Facey et al, 2012).…”

Differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins

“…Three thermophilic archaea (Sulfolobus tokodaii (Kawarabayasi et al, 2001), Archaeoglobus fulgidus (Klenk et al, 1997), Methanopyrus kandleri (Slesarev et al, 2002)), three thermophilic eubacteria (Thermoanaerobacter tengcongensis (Bao et al, 2002), Thermotoga maritima (Nelson et al, 1999), Thermus thermophilus HB8 (GenBank: AP008226.1)), three mesophilic archaea (Methanosphaera stadtmanae (Fricke et al, 2006), Methanocorpusculum labreanum (Anderson et al, 2009), Halobacterium sp. NRC-1 (Ng et al, 2000)), and three mesophilic eubacteria (Haemophilus influenzae Rd KW20 (Fleischmann et al, 1995), Escherichia coli K12 MG1655 (Blattner et al, 1997), Pseudomonas aeruginosa PA01 (Stover et al, 2000)) were surveyed in this study.…”