Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis

Abstract

The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. The methanogenic Archaea (methanogens) occupy a unique metabolic niche, as they produce methane, which is a useful energy source and a powerful greenhouse gas. These organisms are found in diverse anaerobic habitats, ranging from aquatic and marine sediments to sewage digesters and the rumens and large intestines of herbivores and other mammals (127). In these habitats, the degradation of organic matter results in the production of H 2 and other intermediates by fermentative organisms. By maintaining an extremely low partial pressure of H 2 , the methanogens keep fermentative pathways energetically favorable. In addition, some methanogens may occupy niches where hydrogen is produced predominately by geothermal reactions.Metabolically, methanogens are divided into those that specialize in CO 2 reduction and those that also use acetate and/or methyl compounds. The former group, the hydrogenotrophs, use H 2 as an electron donor to reduce CO 2 to methane. Many hydrogenotrophic species can substitute formate or certain low-molecular-weight alcohols and ketones for H 2 . Complete genome sequences have been published for three hydrogenotrophic methanogens, Methanocaldococcus jannaschii (13), Methanothermobacter thermautotrophicus (105), and Methanopyrus kandleri (104), all of which are thermophiles or hyperthermophiles. Of the methanogens that utilize acetate and methyl compounds, complete genome sequences have been published for two species, Methanosarcina acetivorans (26) and Methanosarcina mazei (19), both of which are mesophiles. In addition, partial sequences have been published for two psychrophiles, the hydrogenotroph Methanogenium frigidum and the methylotroph Methanolobus burtonii (97).Genome sequences of methanogens have answered many questions, but they have inspired many others. More than half of the genes in Methanocaldococcus jannaschii lack a predicted function (13), and this proportion has not declined significantly as other methanogen sequences have been determined. The proportions of genes of unknown functions, which are either homologous to other genes of unknown function...

Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase

“…The β subunits were used for purification as this subunit has been demonstrated to contain the active site for heterodisulfide reduction (8). The M. maripaludis genome encodes two Hdrs (9), and either HdrB1 (strain MM1263) or HdrB2 (strain MM1264) was tagged to determine if there were differences between the protein interactions of each. In addition, we had preliminary evidence (based on early purification experiments) that one of two Fdhs encoded in the M. maripaludis genome might be included in protein complexes with Hdr.…”

Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

“…For instance, the methanogen Methanococcus maripaludis S2 possesses 1,779 genes, only a few of which have been characterized and an even smaller portion of which has been studied in detail. Close to 800 genes remain annotated as hypothetical proteins awaiting proper identification (3). Much of this uncertainty is shared with other archaea, in which many of the fundamental life processes have not been investigated in the same detail as in the bacteria and eukaryotes.…”

Characterization of an NADH oxidase of the flavin-dependent disulfide reductase family from Methanocaldococcus jannaschii

“…The genome of M. jannaschii carries an ORF (MJ0649) that has been annotated as an NADH oxidase (Nox) homologue (Bult et al, 1996) (Fig. 1), and such ORFs are present in most methanogens (Bult et al, 1996;Hendrickson et al, 2004;Smith et al, 1997). Methanogens are strict anaerobes (Boone et al, 1993).…”

“…faecalis NADH peroxidase (P37062; Ross & Claiborne, 1991); EfNox, Ent. faecalis NADH oxidase (CAA48728; Ross & Claiborne, 1992); SaCoADR, S. aureus coenzyme A disulfide reductase (AF041467; delCardayre & Davies, 1998); MmpRbo, Methanococcus maripaludis S2 NAD(P)H : rubredoxin oxidoreductase (MMP1259; Hendrickson et al, 2004); MthNox, Methanothermobacter thermautotrophicus DH Nox (MTH1354; Smith et al, 1997). The fully conserved residues are shown in white and with shading of selected colours.…”

“…Also, in contrast to non-methanogenic anaerobic archaea, which carry three to nine nox homologues (Klenk et al, 1997;Maeder et al, 1999;Robb et al, 2001), M. jannaschii carries only one such ORF (Pagala et al, 2002). Methanothermobacter thermautotrophicus, Methanococcus maripaludis, Methanosarcina acetivorans and Methanosarcina barkeri, which are also methanogens, carry one, one, two, and one Nox homologues, respectively (Galagan et al, 2002;Hendrickson et al, 2004; http://genome.ornl.gov/microbial/mbar/; Smith et al, 1997). Therefore, we are interested in elucidating the role of mj0649, the nox homologue of M. jannaschii.…”