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TitleElectron flow in hydrogenotrophic methanogens under nickel limitation.
Journal, issue, pagesNature, Vol. 644, Issue 8076, Page 490-496, Year 2025
Publish dateJul 2, 2025
AuthorsShunsuke Nomura / Pablo San Segundo-Acosta / Evgenii Protasov / Masanori Kaneko / Jörg Kahnt / Bonnie J Murphy / Seigo Shima /
PubMed AbstractMethanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO ...Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO reduction are generated by a flavin-based electron-bifurcation reaction catalysed by heterodisulfide reductase (Hdr) complexed with the associated [NiFe]-hydrogenase (Mvh). F-reducing [NiFe]-hydrogenase (Frh) provides electrons to the methanogenic pathway through the electron carrier F (ref. ). Here we report that under strictly nickel-limited conditions, in which the nickel concentration is similar to those often observed in natural habitats, the production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly downregulated. The Frh reaction is substituted by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F-dependent electron-donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions. Biochemical and structural characterization of Elp-Hdr complexes confirms the electronic interaction between Elp and Hdr. The conservation of the genes encoding Elp and Hmd in CO-reducing hydrogenotrophic methanogens suggests that the Hmd system is an alternative pathway for electron flow in CO-reducing hydrogenotrophic methanogens under nickel-limited conditions.
External linksNature / PubMed:40604290 / PubMed Central
MethodsEM (single particle)
Resolution1.85 - 2.47 Å
Structure data

EMDB-19530: State 2 Hdr-focused map Elp-Hdr
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-19531: State 2 mobile-arm-focused map Elp-Hdr
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-19532: State 2 Elp-Hdr consensus map
Method: EM (single particle) / Resolution: 2.3 Å

19533

8rvu

EMDB-19533, PDB-8rvu:
CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)
Method: EM (single particle) / Resolution: 2.22 Å

19534

8rvv

EMDB-19534, PDB-8rvv:
CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2, dimer (composite structure)
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-19535: State 1 Hdr-focused map Elp-Hdr
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-19536: State 1 Mobile-arm-focused map Elp-Hdr
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-19537: State 1 Elp-Hdr consensus map
Method: EM (single particle) / Resolution: 2.47 Å

19538

8rvy

EMDB-19538, PDB-8rvy:
CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)
Method: EM (single particle) / Resolution: 2.36 Å

19564

8rwn

EMDB-19564, PDB-8rwn:
CryoEM structure of the Hdr(ABC)2 subunits of the Elp-Hdr complex of Methanothermobacter marburgensis
Method: EM (single particle) / Resolution: 1.85 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

ChemComp-HOH:
WATER

Source
  • methanothermobacter marburgensis (archaea)
KeywordsOXIDOREDUCTASE / Redox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase

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