Pathway of glycogen metabolism in Methanococcus maripaludis

Yu, Jae-Pil; Ladapo, Jonathan; Whitman, William B.

doi:10.1128/jb.176.2.325-332.1994

Cited by 92 publications

(98 citation statements)

References 59 publications

(31 reference statements)

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“…Eha could be involved in 2-ketoglutarate biosynthesis, because 2-ketoglutarate oxidoreductase depends on Fd (9), and high levels of glutamate in the medium (10 mM) could provide sufficient 2-ketoglutarate and remove the requirement for Eha. Alternatively, Eha might be involved in NAD + reduction, and alanine dehydrogenase in methanococci generates NADH (16). However, when glutamate or alanine was added, still no mutations were obtained.…”

Section: Resultsmentioning

confidence: 99%

Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis

Lie

Costa

Lupa

et al. 2012

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

106

114

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Despite decades of study, electron flow and energy conservation in methanogenic Archaea are still not thoroughly understood. For methanogens without cytochromes, flavin-based electron bifurcation has been proposed as an essential energy-conserving mechanism that couples exergonic and endergonic reactions of methanogenesis. However, an alternative hypothesis posits that the energy-converting hydrogenase Eha provides a chemiosmosis-driven electron input to the endergonic reaction. In vivo evidence for both hypotheses is incomplete. By genetically eliminating all nonessential pathways of H 2 metabolism in the model methanogen Methanococcus maripaludis and using formate as an additional electron donor, we isolate electron flow for methanogenesis from flux through Eha. We find that Eha does not function stoichiometrically for methanogenesis, implying that electron bifurcation must operate in vivo. We show that Eha is nevertheless essential, and a substoichiometric requirement for H 2 suggests that its role is anaplerotic. Indeed, H 2 via Eha stimulates methanogenesis from formate when intermediates are not otherwise replenished. These results fit the model for electron bifurcation, which renders the methanogenic pathway cyclic, and as such requires the replenishment of intermediates. Defining a role for Eha and verifying electron bifurcation provide a complete model of methanogenesis where all necessary electron inputs are accounted for. M ethanogenesis is an anaerobic respiration carried out by a phylogenetically related group of Archaea within the phylum Euryarchaeota. Methanogens are divided into two metabolic types, those without and those with cytochromes (1). Methanogens without cytochromes use H 2 as an electron donor and are termed hydrogenotrophic. Some species can substitute H 2 with formate, and a few can use secondary alcohols. CO 2 is the electron acceptor and is reduced to methane. Methanogens with cytochromes reduce certain methyl compounds or the methyl carbon of acetate to methane and are called methylotrophic. Many can also use H 2 and CO 2 , as can hydrogenotrophic methanogens.Although the pathways of methanogenesis have long been known, an understanding of energy conservation has been slower to emerge. Methanogens with and without cytochromes both export Na + when a methyl group is transferred from the carrier tetrahydromethanopterin (H 4 MPT) to coenzyme M (CoM) (Fig. 1). The Na + gradient across the membrane is used directly for ATP synthesis or is converted by an antiporter to a proton gradient. However, for methanogenesis from CO 2 , the initial reduction of CO 2 to a formyl group attached to methanofuran (MFR) is endergonic. How energy is provided to drive this reaction is not well understood. Methanogens with and without cytochromes have membrane-associated energy-converting hydrogenases that couple the reduction of low-potential ferredoxins (Fd) to a chemiosmotic membrane gradient (2). If such a Fd donates electrons for CO 2 reduction, an energy-converting hydrogenase is the conduit of ener...

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Section: Resultsmentioning

confidence: 99%

Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis

Lie

Costa

Lupa

et al. 2012

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

106

114

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“…It is an undisputed fact that glycolysis and glucogenesis are almost as widespread among archaea, bacteria, and eukaryotes as are ribosomes (46,99,161,164,165,194). Furthermore, even the facultatively autotrophic archaeon Methanococcus maripalusis has its versions of these enzymes (207). Accordingly, it is not clear what problem is solved by speculating that a methanogenic archaeon was the beneficiary of a transfer of genes for heterotrophy from the ancestral ␣-proteobacterial endosymbiont (124).…”

Section: Eukaryotic Heterotrophymentioning

confidence: 99%

Origin and Evolution of the Mitochondrial Proteome

Kurland

Andersson

2000

Microbiol Mol Biol Rev

362

272

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SUMMARY The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral α-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from α-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the α-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific α-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.

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“…Although Class I and Class II FBP aldolase activities have been demonstrated in Archaea (15)(16)(17)(18)(19)(20)(21), no genes encoding classical Class I or II enzymes have been identified in any of the sequenced archaeal genomes suggesting that Archaea possess novel types of aldolases that are either absent or not yet recognized as such in Bacteria and Eucarya. The latter is supported by initial data base searches of Galperin et al (22) who identified gene homologs of the unusual Class I FBP aldolase gene (dhnA) of E. coli in the sequenced archaeal genomes.…”

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confidence: 99%

Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I Aldolase

Siebers

Brinkmann

Dörr

et al. 2001

Journal of Biological Chemistry

101

102

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Fructose-1,6-bisphosphate (FBP) aldolase activity has been detected previously in several Archaea. However, no obvious orthologs of the bacterial and eucaryal Class I and II FBP aldolases have yet been identified in sequenced archaeal genomes. Based on a recently described novel type of bacterial aldolase, we report on the identification and molecular characterization of the first archaeal FBP aldolases. We have analyzed the FBP aldolases of two hyperthermophilic Archaea, the facultatively heterotrophic Crenarchaeon Thermoproteus tenax and the obligately heterotrophic Euryarchaeon Pyrococcus furiosus. For enzymatic studies the fba genes of T. tenax and P. furiosus were expressed in Escherichia coli. The recombinant FBP aldolases show preferred substrate specificity for FBP in the catabolic direction and exhibit metal-independent Class I FBP aldolase activity via a Schiff-base mechanism. Transcript analyses reveal that the expression of both archaeal genes is induced during sugar fermentation. Remarkably, the fbp gene of T. tenax is co-transcribed with the pfp gene that codes for the reversible PP i -dependent phosphofructokinase. As revealed by phylogenetic analyses, orthologs of the T. tenax and P. furiosus enzyme appear to be present in almost all sequenced archaeal genomes, as well as in some bacterial genomes, strongly suggesting that this new enzyme family represents the typical archaeal FBP aldolase. Because this new family shows no significant sequence similarity to classical Class I and II enzymes, a new name is proposed, archaeal type Class I FBP aldolases (FBP aldolase Class IA).Fructose-1,6-bisphosphate (FBP) 1 aldolase (EC 4.1.2.13) catalyzes the reversible aldol condensation of glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) yielding FBP. The enzyme fulfills an amphibolic function being involved in catabolic (glycolysis) as well as anabolic pathways (gluconeogenesis and Calvin cycle). In spite of this central function in carbohydrate metabolism, up to now no archaeal genes coding for the respective enzyme activities have been analyzed.Two distinct classes of FBP aldolases occur in nature, which differ in their enzymatic mechanisms (1-4). Class I FBP aldolases form a Schiff-base intermediate between the carbonyl substrate (FBP and DHAP) and the ⑀-amino group of the active site lysine residue and are inactivated by borohydride (NaBH 4 ), whereas Class II FBP aldolases depend on divalent metal ions to stabilize the carbanion intermediate and are, therefore, inhibited by EDTA. Class II enzymes of bacterial and eucaryal origin generally form dimers with a subunit molecular mass of ϳ40 kDa, whereas the Class I pendants are heterogeneous. Eucaryal aldolases are homomeric tetramers with a subunit molecular mass of ϳ40 kDa, and for bacterial enzymes oligomeric arrangements from monomer to decamer and subunit molecular masses of 27-40 kDa have been described (5, 6).Sequence comparisons of Class I and II FBP aldolases revealed no detectable sequence homology, suggesting convergent evolut...

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Pathway of glycogen metabolism in Methanococcus maripaludis

Cited by 92 publications

References 59 publications

Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis

Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis

Origin and Evolution of the Mitochondrial Proteome

Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I Aldolase

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