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The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis - PubMed

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The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis

Wolfgang F Fricke et al. J Bacteriol. 2006 Jan.

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 H2 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/acetyl-coenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO2 to methane or oxidize methanol to CO2 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. Seventy-three 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.

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Figures

FIG. 1.
FIG. 1.

Circular map of the chromosome of M. stadtmanae. Rings from the outside to the inside: scale (in base pairs), protein-encoding sequences (blue or yellow), CDS with gene homologues in M. thermautotrophicus (magenta), putative highly expressed CDS (green), G+C content variation (higher values on the outside), rRNA and tRNA coding sequences (red), and cdc6 genes (black).

FIG. 2.
FIG. 2.

Metabolic pathways involved in methanol reduction to methane with H2 and in C1 unit biosynthesis from C-2 of acetate in M. stadtmanae. The genes encode the following enzymes (see text): ehb, energy-converting hydrogenase; por, pyruvate:ferredoxin oxidoreductase; ppsA, phosphoenolpyruvate synthase; eno, enolase; apg, phosphoglycerate mutase; serA, phosphoglycerate dehydrogenase; glyA, serine:H4MPT hydroxymethyl transferase; hps, hexulose phosphate synthase; fae, formaldehyde-activating enzyme; fwd, formylmethanofuran dehydrogenase; ftr, formylmethanofuran:H4MPT formyltransferase; mch, methenyl-H4MPT cyclohydrolase; fprA, F420H2 oxidase; fno, F420H2:NADP oxidoreductase; mtd, methylene-H4MPT dehydrogenase; thyA, thymidylate synthase; frh, F420-reducing hydrogenase; mer, methylene-H4MPT reductase; metE, methionine synthase; mtr, methyl-H4MPT:coenzyme M methyltransferase; mta, methanol:coenzyme M methyltransferase; mvh, non-F420-reducing hydrogenase; hdr, heterodisulfide reductase; and mrt, methyl-coenzyme M reductase. PEP, phosphoenolpyruvate; 2-PGA, 2-phosphoglycerate; 3-PGA, 3-phosphoglycerate; FBP, fructose bisphosphate; F6P, fructose-6-phosphate; Hu6P, 3-hexulose-6-phosphate; CHO-MFR, formylmethanofuran; Ru5P, ribulose-5-phosphate.

FIG. 3.
FIG. 3.

Topological model of the HdrABC/MvhADG complex catalyzing the reduction of CoM-S-S-CoB with H2 in a proton-translocating reaction in M. stadtmanae. In the model it is assumed that based on indirect evidence, HdrB is an integral membrane protein, although this is not reflected in its primary structure (see text).

FIG. 4.
FIG. 4.

Schematic representation of the 37 putative proteins encoded by the group of large CDS with a repetitive structure in M. stadtmanae. (a) General composition shared by all proteins of this group, including an N-terminal leader sequence (yellow) followed by a predicted transmembrane (TM) helix (blue) and by a variable number of repeated peptide sequences (green and red). (b) Schematic composition of the three largest proteins of this group (Msp0762 protein, 3,357 amino acids [aa]; Msp0568 protein, 2,980 aa; Msp0597 protein, 2,469 aa). Two of these, the Msp0568 and Msp0597 proteins, are unique to M. stadtmanae; only the Msp0762 protein exhibits homology to bacterial proteins (Table 4). The short leader sequence is Lys and Asn rich, typically having the form MKNK. At least one copy of a short sequence motif is found at the C terminus of all proteins in this group [G(K/R)XXXKXNGRT]. Sequence variations of repetitive peptide sequences are indicated by green. Repetitive peptides of different large CDS do not necessarily have the same sequence.

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