identifier: METPO:1000800
label: respiration
definition: A metabolism that is characterized by the method of performing cellular
  respiration, distinguished primarily by the specific terminal electron acceptor
  utilized for producing cellular energy.
definition_source: DOI:10.1016/j.bbabio.2008.09.008
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000060
synonyms:
- synonym_text: pathways
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Anthea Guo
evidence:
- reference: DOI:10.1016/j.bbabio.2008.09.008
  snippet: membrane-bound electron transport chain
  notes: Review supports respiratory redox chains producing ion gradients and ATP.
- reference: DOI:10.1128/mmbr.61.4.533-616.1997
  snippet: oxygen as terminal electron acceptor
  notes: Review contrasts aerobic respiration with anaerobic use of alternative acceptors.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "aerobic and anaerobic respiration"
  reference: PMID:25268772
- taxon_id: NCBITaxon:266
  taxon_label: Paracoccus denitrificans
  note: "respiratory model"
  reference: PMID:41591903
causal_graphs:
- graph_id: respiration_electron_acceptor_energy_conservation
  title: Respiration electron acceptor energy conservation
  description: DOI-backed graph linking electron donors, terminal electron acceptors,
    membrane electron transport, proton motive force, and ATP synthesis.
  nodes:
  - node_id: respiration_trait
    label: respiration
    node_type: TRAIT
    grounding: METPO:1000800
    description: Energy metabolism using electron transport to a terminal electron
      acceptor.
  - node_id: electron_donor
    label: electron donor
    node_type: CHEMICAL
    description: Reduced substrate supplying electrons.
    grounding: CHEBI:15022
  - node_id: terminal_electron_acceptor
    label: terminal electron acceptor
    node_type: CHEMICAL
    description: Oxidized substrate receiving electrons at the end of a respiratory
      chain.
    grounding: METPO:1007504
  - node_id: oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Aerobic terminal electron acceptor.
  - node_id: nitrate
    label: nitrate
    node_type: CHEMICAL
    grounding: CHEBI:17632
    description: Alternative anaerobic terminal electron acceptor.
  - node_id: membrane_electron_transport_chain
    label: membrane electron transport chain
    node_type: PATHWAY
    description: Membrane redox chain conserving energy from donor-to-acceptor electron
      flow.
    grounding: GO:0022900
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical ion gradient generated across a coupling membrane.
    grounding: METPO:1007500
  - node_id: atp_synthase
    label: ATP synthase
    node_type: GENE_OR_PROTEIN
    description: Enzyme complex using proton motive force for ATP synthesis.
    grounding: UniProtKB:A0A415TT77
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier produced by respiration.
  - node_id: complex_i
    label: respiratory Complex I (NADH:quinone oxidoreductase)
    node_type: GENE_OR_PROTEIN
    description: NADH dehydrogenase that oxidizes NADH, reduces quinone, and pumps
      protons (~4 H+/2e-).
  - node_id: anoxic_microsites
    label: anoxic microsites
    node_type: ENVIRONMENTAL_FACTOR
    description: Localized oxygen-depleted zones that constrain available terminal
      electron acceptors.
  - node_id: oxygen_depletion
    label: oxygen depletion
    node_type: ENVIRONMENTAL_FACTOR
    description: Decline of O2 below physiological thresholds in a microenvironment.
  - node_id: anaerobic_respiration
    label: anaerobic respiration
    node_type: BIOLOGICAL_PROCESS
    description: Respiration using alternative (non-oxygen) terminal electron acceptors.
    grounding: GO:0009061
  edges:
  - subject: respiration_trait
    predicate: uses electron flow from
    object: electron_donor
    description: Respiration begins with reduced electron donors.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: free energy of a redox reaction
      notes: Supports respiratory energy conservation from redox reactions.
  - subject: electron_donor
    predicate: transfers electrons to
    object: terminal_electron_acceptor
    description: Electrons move from donors to terminal acceptors.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: electron transfer process
      notes: Supports donor-to-acceptor electron flow in respiratory chains.
    predicate_id: METPO:2007403
  - subject: oxygen
    predicate: example of
    object: terminal_electron_acceptor
    description: Oxygen is the terminal electron acceptor in aerobic respiration.
    evidence:
    - reference: DOI:10.1128/mmbr.61.4.533-616.1997
      snippet: oxygen as terminal electron acceptor
      notes: Supports oxygen as a respiratory terminal acceptor.
    predicate_id: rdfs:subClassOf
  - subject: nitrate
    predicate: example of
    object: terminal_electron_acceptor
    description: Nitrate is a representative anaerobic terminal electron acceptor.
    evidence:
    - reference: DOI:10.1128/mmbr.61.4.533-616.1997
      snippet: utilization of nitrate
      notes: Supports nitrate use in anaerobic respiration.
    predicate_id: rdfs:subClassOf
  - subject: membrane_electron_transport_chain
    predicate: couples electron flow to
    object: proton_motive_force
    description: Respiratory chains conserve redox energy as an ion gradient.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: generation of an electrochemical ion gradient
      notes: Supports ion-gradient generation by membrane electron transport.
    predicate_id: METPO:2007602
  - subject: proton_motive_force
    predicate: regulates
    object: atp_synthase
    description: Proton motive force powers ATP synthase.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: drives ATP synthesis
      notes: Supports ATP synthase as the downstream energy-conservation output.
    predicate_id: RO:0002211
  - subject: atp_synthase
    predicate: produces
    object: atp
    description: ATP synthase produces ATP during respiration.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: ATP synthesis
      notes: Supports ATP production from respiratory energy conservation.
    predicate_id: METPO:2000202
  - subject: complex_i
    predicate: contributes to
    object: proton_motive_force
    description: Complex I pumps protons during NADH oxidation/quinone reduction,
      building the proton motive force.
    evidence:
    - reference: DOI:10.3390/ijms252413421
      notes: Complex I pumps four protons per pair of electrons, contributing to the
        formation of a proton motive force.
    predicate_id: RO:0002326
  - subject: anoxic_microsites
    predicate: controls
    object: terminal_electron_acceptor
    description: Anoxic microsites control the local availability and ordering of
      terminal electron acceptors.
    evidence:
    - reference: DOI:10.1021/acsearthspacechem.3c00032
      notes: Microsites control the local availability and ordering of terminal electron
        acceptors (O2, NO3-, Fe(III), Mn(IV), SO4 2-).
    predicate_id: RO:0002211
  - subject: oxygen_depletion
    predicate: enables
    object: anaerobic_respiration
    description: When O2 falls below physiological thresholds, cells shift to alternative
      acceptors and perform anaerobic respiration.
    evidence:
    - reference: DOI:10.1021/acsearthspacechem.3c00032
      notes: When O2 falls below physiological thresholds, microorganisms shift to
        alternative electron acceptors and carry out anaerobic respiration.
    predicate_id: RO:0002327
  - subject: anaerobic_respiration
    predicate: subtype of
    object: respiration_trait
    description: Anaerobic respiration is a form of respiration distinguished by its
      terminal electron acceptor.
    evidence:
    - reference: DOI:10.1128/mmbr.61.4.533-616.1997
      notes: Review contrasts aerobic respiration with anaerobic use of alternative
        acceptors.
curation_history:
- timestamp: '2026-05-05T01:35:46.910466+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-08T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for donor-to-acceptor respiratory electron
    flow, membrane ion-gradient generation, and ATP synthesis.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:49Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×2).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007403×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    drives → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007504×1, METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A415TT77×1).
  llm_assisted: true
- timestamp: '2026-05-24T08:14:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17499×1, GO:0022900×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:13Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
  llm_assisted: true
- timestamp: '2026-06-14T07:26:19Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007602×1).
  llm_assisted: true
- timestamp: '2026-06-15T07:19:08Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
    fix; verified vs OAK).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×1, RO:0002211×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009061×1).
  llm_assisted: true