Genetics of <i>Methanococcus</i>: possibilities for functional genomics in Archaea

Tumbula, Debra L.; Whitman, William B.

doi:10.1046/j.1365-2958.1999.01463.x

Cited by 63 publications

(41 citation statements)

References 41 publications

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“…Another property of bacterial populations is that genetic rearrangements frequently occur, often related to environmental changes (Madigan et al, 2000 ;Wright, 2000). Genetic recombination processes are less studied in the Archaea than in the Bacteria (Tumbula & Whitman, 1999), but the high phenotypic and evolutionary diversity of representatives within the Archaea makes it likely that genetic recombination processes are no less frequent within this group compared to the Bacteria. As to the view of population structure, it is unknown how often very narrow and rarely isolated bacterial species exist in nature.…”

Section: Bacterial Population Structure and Strategy Of Classificationmentioning

confidence: 99%

Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).

Christensen¹,

Bisgaard²,

Frederiksen³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

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Since an exponential increase in new taxa can be expected in the future, the authors discuss problems related to naming new species and genera based upon descriptions of a single isolate and suggest that this practice is re-evaluated. It is proposed that the following should be added to Recommendation 30b of the Bacteriological Code : ' Descriptions should be based on as many strains as possible (minimum five), representing different sources with respect to geography and ecology in order to be well characterized both phenotypically and genotypically, to establish the centre (from which the type strain could be chosen) and the extent of the cluster to be named. In addition, comparative studies should be performed, including reference strains that represent neighbouring species and/or genera, in order to give descriptions that are sufficiently detailed to allow differentiation from these neighbours. '

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Section: Bacterial Population Structure and Strategy Of Classificationmentioning

confidence: 99%

Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).

Christensen¹,

Bisgaard²,

Frederiksen³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

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“…To this end, we performed experiments with the hydrogenotrophic methanogen, Methanococcus maripaludis. M. maripaludis is ideal for such an undertaking because of its rapid growth under laboratory conditions, a well-developed set of genetic tools (3,4), the ability to grow in continuous culture under conditions of defined nutrient limitation (5), and the availability of an exhaustive dataset from quantitative measurements of the proteome (6,7).…”

mentioning

confidence: 99%

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

Costa

Wong

Wang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

172

183

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In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F 420 -nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electronbifurcation model of energy conservation, the composition of the complex also suggests that either H 2 or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H 2 via F 420 -nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H 2 as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F 420 -nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H 2 , is closely integrated into the methanogenic pathway.energy conservation | Archaea | formate dehydrogenase | formylmethanofuran dehydrogenase | F 420 -nonreducing hydrogenase T he biochemical steps in methanogenesis from CO 2 are well known, but the interactions that lead to net energy conservation are not well understood. The steps in the pathway are diagrammed in Fig. 1 (1). The first step involves the reduction of CO 2 and covalent attachment to a unique cofactor, methanofuran (MFR), via the action of formylmethanofuran dehydrogenase (Fwd) to generate formyl-MFR. This represents an energy-consuming step in the pathway and is dependent on reduced ferredoxin, thought to be produced at the expense of a chemiosmotic membrane potential via the energy-conserving hydrogenase, Eha. Next, the formyl group is transferred to another carrier, tetrahydromethanopterin (H 4 MPT), and is then reduced to generate methyl-H 4 MPT. The methyl group is then transferred to yet another carrier, coenzyme M (HS-CoM), by methyl-H 4 MPT-CoM methyltransferase (Mtr) to generate methyl-S-CoM. At this point, Na + ions are translocated across the cell membrane. The final step involves reduction of the methyl group to CH 4 and capture of HS-CoM by coenzyme B (HS-CoB) to form a CoM-S-S-CoB heterodisulfide. To regenerate HS-CoM and HS-CoB, another enzyme is used, heterodisulfid...

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“…A hydrogenotrophic methanogen, M. maripaludis generates methane from hydrogen and carbon dioxide or formate. Relatively rapid growth (13), genetic tools (25), and a complete genome sequence (11) contribute to the utility of M. maripaludis as a laboratory model. Numerous mutants have been generated by positive selection for homologous recombination leading to genetic insertion or gene replacement (e.g., see references 17 and 20).…”

mentioning

confidence: 99%

Markerless Mutagenesis inMethanococcus maripaludisDemonstrates Roles for Alanine Dehydrogenase, Alanine Racemase, and Alanine Permease

2005

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Among the archaea, Methanococcus maripaludis has the unusual ability to use L-or D-alanine as a nitrogen source. To understand how this occurs, we tested the roles of three adjacent genes encoding homologs of alanine dehydrogenase, alanine racemase, and alanine permease. To produce mutations in these genes, we devised a method for markerless mutagenesis that builds on previously established genetic tools for M. maripaludis. The technique uses a negative selection strategy that takes advantage of the ability of the M. maripaludis hpt gene encoding hypoxanthine phosphoribosyltransferase to confer sensitivity to the base analog 8-azahypoxanthine. In addition, we developed a negative selection method to stably incorporate constructs into the genome at the site of the upt gene encoding uracil phosphoribosyltransferase. Mutants with in-frame deletion mutations in the genes for alanine dehydrogenase and alanine permease lost the ability to grow on either isomer of alanine, while a mutant with an in-frame deletion mutation in the gene for alanine racemase lost only the ability to grow on D-alanine. The wild-type gene for alanine dehydrogenase, incorporated into the upt site, complemented the alanine dehydrogenase mutation. Hence, the permease is required for the transport of either isomer, the dehydrogenase is specific for the L isomer, and the racemase converts the D isomer to the L isomer. Phylogenetic analysis indicated that all three genes had been acquired by lateral gene transfer from the low-moles-percent G؉C gram-positive bacteria.

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Genetics of Methanococcus: possibilities for functional genomics in Archaea

Cited by 63 publications

References 41 publications

Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).

Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision).

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

Markerless Mutagenesis inMethanococcus maripaludisDemonstrates Roles for Alanine Dehydrogenase, Alanine Racemase, and Alanine Permease

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