Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

Abstract

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-IMRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-IMRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-IMRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.

Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments

“…This residue may play a role in pumping but, as of now, it is Table 3. Amino acid alignment of AtpCK demonstrating the two conserved glutamine (Q) and tyrosine (Y) residues (shown in bold) (identified by: McMillan et al, 2011;Mulkidjanian et al, 2008;Sakai et al, 2011) that appear to be unique for methanogens predicted to have sodium-driven ATPases versus those predicted to have proton-driven or sodium-proton driven ATPases M. boonei is shaded in grey. Organisms predicted to have proton-driven ATPases are shown in red font and those predicted to have sodium-driven ATPases are shown in blue font.…”

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

“…Thereafter, two more isolates, M. arvoryzae MRE50 and M. conradii HZ254, were obtained from Italian and Chinese rice field soils, respectively (27,28). The whole-genome sequences of all three strains are now available (29)(30)(31). Of the three strains, M. conradii HZ254 shows the fastest growth, with a doubling time of 6.5 to 7.8 h under optimum conditions (27).…”

A metaproteomic approach for identifying proteins in anaerobic bioreactors converting coal to methane

“…In terms of CO 2 reduction, three out of the six enzymes dedicated for CO 2 reduction were observed. These enzymes were: formyl-methanofuran dehydrogenase (Fmd, the first enzyme in CO 2 reduction (Sakai et al, 2011)); methylene tetrahydromethanopterin (H 4 MPT) dehydrogenase (Mtd; the fourth enzyme in CO 2 reduction); and methylene tetrahydromethanopterin (H 4 MPT) reductase (Mer, the fifth enzyme in CO 2 reduction). In addition, four different protein families of methanol-5-hydroxybenzimidazolylcobamide methyltransferase were identified.…”

“…Furthermore, two families (gi|490139462, gi|499768063) of formate dehydrogenase resembling that in Methanofollis liminatans and Methanospirillum hungatei, respectively, were detected. These proteins can oxidize formate to CO 2 (Sakai et al, 2011). The second group was 27 protein families that were related to cellular metabolism.…”