TraitMech

TraitMech › METABOLISM

Electron transfer

METPO:1000805 · CLASS · REVIEWED

A metabolism in which electrons are transferred from an electron donor to an electron acceptor.

Trait evidence (2)

Electron transfer redox carrier mechanism

DOI-backed graph for electron donor/acceptor chemistry, redox proteins, membrane electron transport, and extracellular electron-transfer structures.

MECHANISTIC · This is a composite graph spanning respiratory-chain and extracellular electron-transfer modules. The MtrC example supports the S. oneidensis MR-1 extracellular branch only; it does not ground the generic respiratory complexes or imply that MtrC participates in all electron-transfer traits.

Electron transfer redox carrier mechanism Interactive directed graph showing evidence-backed causal relationships for Electron transfer.

Edge evidence

  • Electron transfer transfers electrons from electron donor

    Electron transfer starts from an electron donor.

  • electron donor transfers electrons to electron acceptor METPO:2007403

    Electron transfer moves reducing equivalents from donor to acceptor.

  • redox protein mediates transfer between electron donor

    Redox proteins mediate biological electron-transfer steps.

  • c-type cytochrome example of redox protein rdfs:subClassOf

    c-type cytochromes are electron-transfer proteins.

  • membrane electron transport chain performs terminal acceptor reduction

    Electron transport chains deliver electrons to terminal acceptors.

  • extracellular electron transfer uses structure microbial nanowire

    Some microbes use conductive appendages or nanowires for extracellular electron transfer.

  • extracellular electron transfer uses protein c-type cytochrome

    Extracellular electron transfer can use c-type cytochromes.

  • NADH dehydrogenase (Complex I) reduces ubiquinone METPO:2007802

    Complex I oxidizes NADH and reduces ubiquinone in the respiratory chain.

  • NADH dehydrogenase (Complex I) translocates proton motive force

    Complex I couples NADH:ubiquinone oxidoreduction to transmembrane proton translocation, generating the PMF.

    • DOI:10.3390/ijms252413421 Coupling of redox reaction to vectorial translocation of four protons to generate proton motive force.
  • ubiquinol donates electrons to cytochrome bc1 complex METPO:2007403

    Ubiquinol delivers electrons from the quinone pool to the cytochrome bc1 complex.

  • cytochrome bc1 complex transfers electrons to cytochrome c METPO:2007403

    The bc1 complex passes electrons onward to mobile cytochrome c.

  • cytochrome c transfers electrons to terminal oxidase METPO:2007403

    Cytochrome c delivers electrons to the terminal oxidase (Complex IV).

  • terminal oxidase reduces oxygen METPO:2007802

    The terminal oxidase reduces molecular oxygen to water in aerobic respiration.

  • membrane electron transport chain contributes to Electron transfer RO:0002326

    A membrane electron-transport chain is a principal cellular electron-transfer system.

  • NADH dehydrogenase (Complex I) participates in membrane electron transport chain biolink:participates_in

    Complex I is an entry enzyme of the membrane respiratory electron-transport chain.

  • cytochrome c example of c-type cytochrome rdfs:subClassOf

    Cytochrome c is a mobile member of the cytochrome electron-carrier class.

    • DOI:10.1073/pnas.2307093120 electrons flow to the bc1 complex and onward via cytochrome c Verified against the free public article text.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
c-type cytochrome UniProtKB:Q8EG34
Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC (mtrC) 		Shewanella oneidensis MR-1
NCBITaxon:211586 		UNREVIEWED
retrieved 2026-08-24 · entry v125 · sequence v1

MtrC-family c-type cytochrome mediating extracellular electron transfer to Fe(III) and Mn(IV) acceptors in S. oneidensis MR-1.

  • DOI:10.1073/pnas.0604517103 The decaheme c-type cytochrome MtrC (SO1778) had been implicated in efficient reduction of Fe(III) and Mn(IV) by MR-1. The primary study supports the extracellular electron-transfer role. UniProtKB Q8EG34 is the exact unreviewed MtrC entry from reference proteome UP000008186 and verifies the strain taxon.

Provenance

Identifier source
METPO (2026-06-12)
Author
Jed Dongjin Kim-Ozaeta
Definition source
DOI:10.1016/j.bbabio.2008.09.008

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000805 [-0.425, -0.393, -1.506, +0.156, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/metabolism/electron_transfer-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation-focused research report: microbial electron transfer

## Trait record and scope

- **Trait label:** Electron transfer
- **Trait identifier:** **“METPO:1000805”**
- **Category / kind / status:** METABOLISM / CLASS / REVIEWED
- **Definition:** “A metabolism in which electrons are transferred from an electron donor to an electron acceptor.”
- **Parent:** METPO:1000060

### Recommended interpretation

This trait should represent the **physiological capacity for organized donor-to-acceptor electron flow**, not every isolated oxidation–reduction reaction. Its central causal pattern is:

**electron-donor oxidation → reduced carrier(s) → redox enzyme/chain → electron acceptor reduction**, sometimes coupled to proton- or sodium-motive force and ATP synthesis. Multiheme cytochromes, quinones, flavins, iron–sulfur proteins, NAD(P)H, ferredoxin, and electrodes can serve as intermediate carriers or interfaces. Authoritative reviews describe respiratory electrons moving successively between redox centers, with released energy generating proton motive force and ultimately driving ATP synthase. (edwards2020roleofmultiheme pages 1-2)

**In scope:** aerobic and anaerobic respiratory electron-transfer chains; photosynthetic chains; extracellular electron transfer (EET) to or from minerals, humic substances, electrodes, or cells; direct interspecies electron transfer (DIET); and electron bifurcation when donor-to-two-acceptor flow is explicitly demonstrated.

**Not synonymous with the trait:** respiration, oxidative phosphorylation, EET, DIET, fermentation, metal reduction, or electricity production. These are narrower pathways, outcomes, or assays. Fermentation can include internal redox balancing without an external terminal acceptor. IET through diffusible H₂ or formate is not DIET. Electron bifurcation is a specialized energy-coupling mechanism in which a two-electron donor supplies high- and low-potential one-electron acceptors; flavin-based systems are chiefly found in strict anaerobes and can generate reduced ferredoxin/flavodoxin for difficult reductions or ion-gradient formation. (buckel2018flavinbasedelectronbifurcation pages 1-2)

### Assay interpretation

A positive phenotype may be observed as growth coupled to donor/acceptor pairs, acceptor reduction, donor oxidation, current production or consumption, cyclic voltammetry, redox spectroscopy, membrane-potential formation, or genetic dependence. Current alone is insufficient unless biological electron flow is separated from abiotic electrochemistry. Likewise, a redox-enzyme annotation alone should not establish the organism-level trait.

## Candidate graph architecture

A robust graph should use a conserved core and attach taxon-specific modules:

1. **Core intracellular module:** donor oxidation → NADH/NADPH, ferredoxin/flavodoxin, or electron-transfer flavoprotein → membrane quinone/quinol pool.
2. **Energy-conserving membrane module:** quinol/dehydrogenase or respiratory complex → proton or sodium motive force → ATP synthase.
3. **Terminal-acceptor module:** quinol/cytochrome/ferredoxin → terminal oxidase or reductase → O₂, fumarate, nitrate, sulfate-related intermediates, Fe(III), or another acceptor.
4. **Gram-negative EET module:** inner membrane quinone pool → CymA/CbcL/ImcH → periplasmic cytochromes → porin–cytochrome or nanowire pathway → mineral/electrode/cell.
5. **Mediator module:** intracellular chain → secreted flavin/phenazine or environmental humic shuttle → extracellular acceptor.
6. **DIET module:** donor organism → conductive protein/material interface → recipient organism → recipient terminal reduction.

## Candidate nodes grouped by type

### Trait and biological-process nodes

- Electron transfer — **“METPO:1000805”**
- Electron transport chain — **GO:0022900**
- Respiratory electron transport chain — **GO:0022904**
- Aerobic respiration — **GO:0009060**
- Anaerobic respiration — **GO:0009061**
- Oxidative phosphorylation — **GO:0006119**
- Proton motive force — label plus **GO:0015988** where represented as proton-coupled ATP synthesis
- Extracellular electron transfer — label-only candidate; verify an appropriate METPO/GO term before release
- Direct interspecies electron transfer — label-only candidate
- Flavin-based electron bifurcation — label-only candidate
- Biofilm formation — **GO:0042710**

### Chemicals, donors, acceptors, and cofactors

- NADH — **CHEBI:16908**
- NAD⁺ — **CHEBI:15846**
- NADPH — **CHEBI:16474**
- Molecular oxygen — **CHEBI:15379**
- Water — **CHEBI:15377**
- Proton — **CHEBI:15378**
- Fumarate — **CHEBI:18012**

Showing the first 60 of 246 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (3)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for donor-to-acceptor electron transfer, redox proteins, cytochromes, membrane chains, and extracellular nanowire-associated transfer.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403×1).

  5. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A076EJF0×1, UniProtKB:A0A072TMC1×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17499×1, GO:0022900×1).

  7. · FIX_NODE_GROUNDING_CURIE · claude

    Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK).

  8. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report.

  9. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007403×3, METPO:2000017×2).

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17976×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A061JR98×1, UniProtKB:A0A2U9ILE5×1).

  12. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 3 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  13. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 2 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to reduces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.

  14. · NORMALISE_NODE_TYPE · claude

    Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: BIOLOGICAL_PROCESS -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.

  15. · NORMALISE_NODE_SENSE · claude

    One node_id per SENSE (issues 356, 384): molecular_oxygen is the chemical sense here. The molecule, not the condition — the dioxygen participating in the reaction the graph describes. Normalised onto molecular_oxygen, the id 20 other chemical occurrences already use, so one id means one sense corpus-wide (issues 356, 384).

  16. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).

  17. · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex

    Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).

  18. · CURATE_PROTEIN_TAXON_EXAMPLE · codex

    Added a DOI-backed S. oneidensis MR-1 MtrC example, grounded Complex I to the current GO complex term, recorded explicit reviewed label-only dispositions for the remaining broad protein labels, and documented the graph's composite respiratory/EET scope.

  19. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.