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Literature summary extracted from

  • Holmes, D.; Rotaru, A.; Ueki, T.; Shrestha, P.; Ferry, J.; Lovley, D.
    Electron and proton flux for carbon dioxide reduction in Methanosarcina barkeri during direct interspecies electron transfer (2018), Front. Microbiol., 9, 3109 .
    View publication on PubMedView publication on EuropePMC

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.12.98.1 membrane transmembrane protein Geobacter metallireducens 16020
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Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri
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 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri MS
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 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri DSM 800
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 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri MS DSM 800
-
 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri
-
 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri MS
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 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri DSM 800
-
 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ Methanosarcina barkeri MS DSM 800
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 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.12.98.1 H2 + oxidized coenzyme F420 Geobacter metallireducens
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 reduced coenzyme F420
-
 ?
1.12.98.1 additional information Geobacter metallireducens generation of F420H2 by Fpo with electrons derived from DIET requires an abundance of reduced methanophenazine ?
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Organism

EC Number Organism UniProt Comment Textmining
1.5.7.2 Methanosarcina barkeri
-
-
-
1.8.98.4 Methanosarcina barkeri
-
-
-
1.8.98.4 Methanosarcina barkeri DSM 800
-
-
-
1.8.98.4 Methanosarcina barkeri MS
-
-
-
1.8.98.5 Methanosarcina barkeri
-
-
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1.8.98.5 Methanosarcina barkeri MS DSM 800
-
-
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1.12.98.1 Geobacter metallireducens
-
-
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Source Tissue

EC Number Source Tissue Comment Organism Textmining
1.8.98.4 cell culture coculture of Methanosarcina barkeri with Geobacter metallireducens, transcriptome analysis, overview. Out of the 3809 predicted protein-coding genes in the Methanosarcina barkeri MS genome, 1912 and 1909 genes have expression levels that are higher than the median in DIET-grown cells, respectively Methanosarcina barkeri
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1.8.98.5 cell culture coculture of Methanosarcina barkeri with Pelobacter carbinolicus, transcriptome analysis, overview. Out of the 3809 predicted protein-coding genes in the Methanosarcina barkeri MS genome, 1912 and 1909 genes have expression levels that are higher than the median in HIT-grown cells, respectively Methanosarcina barkeri
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Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri MS 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri DSM 800 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.4 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri MS DSM 800 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri MS 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri DSM 800 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.8.98.5 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
 Methanosarcina barkeri MS DSM 800 2 H2 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
 ?
1.12.98.1 H2 + oxidized coenzyme F420
-
 Geobacter metallireducens reduced coenzyme F420
-
 ?
1.12.98.1 additional information generation of F420H2 by Fpo with electrons derived from DIET requires an abundance of reduced methanophenazine Geobacter metallireducens ?
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-

Synonyms

EC Number Synonyms Comment Organism
1.5.7.2 Fpo
-
 Methanosarcina barkeri
1.12.98.1 F420H2 dehydrogenase
-
 Geobacter metallireducens
1.12.98.1 Fpo
-
 Geobacter metallireducens

Cofactor

EC Number Cofactor Comment Organism Structure
1.8.98.4 coenzyme F420 reduced F420 is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB Methanosarcina barkeri
1.8.98.4 Ferredoxin
-
 Methanosarcina barkeri
1.8.98.5 Ferredoxin
-
 Methanosarcina barkeri

Expression

EC Number Organism Comment Expression
1.5.7.2 Methanosarcina barkeri transcripts for genes for most of the subunits for F420H2 dehydrogenase Fpo are higher in direct interspecies electron transfer-grown cells, i.e. in coculture with Geobacter metallireducens up
1.12.98.1 Geobacter metallireducens transcripts for genes for most of the subunits for the membranebound F420H2 dehydrogenase, Fpo, are higher in direct interspecies electron transfer (DIET)-grown cells compared to hydrogen interspecies electron transfer (HIT) grown cells, overview up

General Information

EC Number General Information Comment Organism
1.5.7.2 metabolism model for electron and proton flux for carbon dioxide reduction to methane in Methanosarcina barkeri during coculture with Geobacter metallireducens. Each two moles of ethanol oxidized to acetate by G. metallireducens releases eight electrons and eight protons. Electrons delivered to methanophenazine in the cell membrane are transferred to Fpo. Proton translocation drives Fpo-catalyzed reduction of F420 to F420H2. Half of the F420H2 produced serves as a reductant in the carbon dioxide reduction pathway. The remaining F420H2 is the electron donor for HdrABC, which reduces ferredoxin and CoM-S-S-CoB in an electron bifurcation reaction Methanosarcina barkeri
1.8.98.4 metabolism generalized model for electron and proton flux during hydrogen interspecies electron transfer (HIT) and direct interspecies electron transfer (DIET) with growth on ethanol as an example, overview. Electron and protons are transported by different mechanisms during DIET. Electron transfer is direct, through e-pili and other electrical contacts. Protons move by diffusion creating a positive proton pressure outside the cell. A mechanism for proton translocation into the cell is required for charge balance in the cytoplasm when cytoplasmic electron acceptors (EA) are reduced and to prevent acidification of the external space between cells. The transcriptome reflects faster growth during HIT and possible greater importance of membrane and outer-surface proteins during DIET. Model for electron and proton flux for carbon dioxide reduction to methane in Methanosarcina barkeri during DIET-based growth, overview Methanosarcina barkeri
1.8.98.4 additional information physiological studies of direct interspecies electron transfer (DIET) require defined co-cultures. Geobacter metallireducens is an environmentally relevant pure culture model for electron-donating partners for DIET because Geobacter species function as the electron-donating partner in important methanogenic environments such as anaerobic digesters and terrestrial wetlands. Studies with defined co-cultures in which Geobacter metallireducens is the electron-donating partner for DIET have suggested that c-type cytochromes and electrically conductive pili [e-pili] facilitate electron transport from Geobacter metallireducens to the electron accepting partner. However, Methanosarcina barkeri, a methanogen shown to participate in DIET, does not possess outer-surface c-type cytochromes or e-pili Methanosarcina barkeri
1.8.98.4 physiological function direct interspecies electron transfer (DIET) is important in diverse methanogenic environments. In DIET, electrically conductive pili [e-pili] and associated electron transport proteins deliver electrons to cytoplasmic electron acceptors. Protons have to be translocated into the cytoplasm for charge balance. The transcriptome of Methanosarcina barkeri grown via DIET in co-culture with Geobacter metallireducens compared with its transcriptome when grown via H2 interspecies transfer (HIT) with Pelobacter carbinolicus shows that transcripts for the F420H2 dehydrogenase (Fpo) and the heterodisulfide reductase, HdrABC, are more abundant during growth on DIET. Electrons delivered to methanophenazine in the cell membrane are transferred to Fpo (cf. EC 1.8.98.1). The external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for Fpo-catalyzed F420 reduction is derived from protons released from Geobacter metallireducens metabolism. Reduced F420 is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB Methanosarcina barkeri
1.8.98.5 metabolism generalized model for electron and proton flux during hydrogen interspecies electron transfer (HIT) and direct interspecies electron transfer (DIET) with growth on ethanol as an example, overview. H2 diffusion shuttles both electrons and protons between cells and carries both electrons and protons into the cell when cytoplasmic electron acceptors are reduced. The transcriptome reflects faster growth during HIT and possible greater importance of membrane and outer-surface proteins during DIET, but no specific upregulation of hydrogenase genes in response to growth via HIT Methanosarcina barkeri
1.8.98.5 physiological function the transcriptome of Methanosarcina barkeri grown via DIET in co-culture with Geobacter metallireducens compared with its transcriptome when grown via H2 interspecies transfer (HIT) with Pelobacter carbinolicus shows that transcripts for the F420H2 dehydrogenase (Fpo) and the heterodisulfide reductase, HdrABC, are more abundant during growth on DIET. In HIT, H2 simultaneously transports both electrons and protons as the H2 diffuses between the two partners. When the H2 is oxidized in the cytoplasm with electron transfer to an electron acceptor, protons are also released and are immediately available to balance the negative charge transferred to the electron acceptor. This maintains charge balance within the cell Methanosarcina barkeri
1.12.98.1 metabolism electrons delivered to methanophenazine in the cell membrane are transferred to Fpo. Proton translocation drives Fpo-catalyzed reduction of F420 to F420H2. Half of the F420H2 produced serves as a reductant in the carbon dioxide reduction pathway. The remaining F420H2 is the electron donor for HdrABC, which reduces ferredoxin and CoM-S-S-CoB in an electron bifurcation reaction. Fpo plays a key role in electron transport for carbon dioxide reduction to methane during direct interspecies electron transfer (DIET) Geobacter metallireducens
1.12.98.1 physiological function the external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for F420H2 dehydrogenase (Fpo)-catalyzed F420 reduction (in Methanosarcina barkeri) is derived from protons released from Geobacter metallireducens metabolism. Enzyme Fpo plays a key role in electron transport for carbon dioxide reduction to methane during direct interspecies electron transfer (DIET). During methylotrophic methanogenesis in Methanosarcina barkeri, Fpo oxidizes F420H2 with the reduction of methanophenazine in the membrane, coupled with vectorial proton translocation to the outside of the membrane. Under some conditions Fpo may catalyze the reverse reaction in which reduced methanophenazine serves as the electron donor for the reduction of F420. In this direction, proton translocation through Fpo into the cytoplasm is required in order to make the reaction thermodynamically favorable. The Fpo-catalyzed reduction of F420 is proton balanced Geobacter metallireducens