Continuous culture of under defined nutrient conditions

Haydock, Andrew; Porat, Iris; Whitman, William B.; Leigh, John A.

doi:10.1016/j.femsle.2004.07.021

Cited by 31 publications

(36 citation statements)

References 24 publications

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“…M. maripaludis strain S52, a leucine auxotroph, has been described (9). Cultures (1-liter volumes) of S52 were grown at 37°C in chemostats as described (9).…”

Section: Methodsmentioning

confidence: 99%

“…Methanococcus maripaludis, a mesophilic hydrogenotrophic methanogen from marine sediments, served as our representative species. As a laboratory model, M. maripaludis is distinguished by relatively rapid growth, a well developed genetic system (5, 6), a complete genome sequence (7), established systems for transcriptome arrays and quantitative proteomics (8), and continuous culture under defined nutrient conditions (9).…”

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confidence: 99%

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Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

Hendrickson

Haydock

Moore

et al. 2007

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

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The use of molecular hydrogen as electron donor for energy generation is a defining characteristic of the hydrogenotrophic methanogens, an ancient group that dominates the phylum Euryarchaeota. We present here a global study of changes in mRNA abundance in response to hydrogen availability for a hydrogenotrophic methanogen. Cells of Methanococcus maripaludis were grown by using continuous culture to deconvolute the effects of hydrogen limitation and growth rate, and microarray analyses were conducted. Hydrogen limitation markedly increased mRNA levels for genes encoding enzymes of the methanogenic pathway that reduce or oxidize the electron-carrying deazaflavin, coenzyme F420. F420-dependent redox functions in energy-generating metabolism are characteristic of the methanogenic Archaea, and the results show that their regulation is distinct from other redox processes in the cell. Rapid growth increased mRNA levels of the gene for an unusual hydrogenase, the hydrogen-dependent methylenetetrahydromethanopterin dehydrogenase.coenzyme F420 ͉ microarrays ͉ Methanococcus maripaludis

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“…M. maripaludis strain S52, a leucine auxotroph, has been described (9). Cultures (1-liter volumes) of S52 were grown at 37°C in chemostats as described (9).…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

Hendrickson

Haydock

Moore

et al. 2007

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

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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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“…Bacterial strains and growth conditions M. maripaludis MM901, wild-type strain S2 with an in-frame deletion of the uracil phosphoribosyltransferase gene (Costa et al 2010), and all gene deletion strains were grown by continuous culture in a 1-L fermenter (New Brunswick Scientific) at 37°C (Haydock et al 2004). Medium and gas compositions were modified from those for excess conditions (Xia et al 2009; Supplemental Table S3).…”

Section: Methodsmentioning

confidence: 99%

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

et al. 2013

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Methanogens catalyze the critical methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and noncoding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 58 different steady-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one noncoding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to intercoordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase-a key enzyme in the methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within methanogenesis as well as between methanogenesis and other cellular functions.

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Continuous culture of under defined nutrient conditions

Cited by 31 publications

References 24 publications

Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea

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

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

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