identifier: METPO:1000801
label: Aerobic respiration
definition: A respiration in which molecular oxygen serves as the terminal electron
  acceptor in the electron transport chain, generating ATP through oxidative phosphorylation
  with water as the final product.
definition_source: DOI:10.1146/annurev.biophys.27.1.329
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000800
synonyms:
- synonym_text: Oxic respiration
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: Oxygen respiration
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1146/annurev.biophys.27.1.329
  snippet: terminal enzyme of respiratory chains
  notes: Review supports cytochrome c oxidase reducing molecular oxygen to water in
    aerobic respiratory chains.
- reference: DOI:10.1016/j.bbabio.2008.09.008
  snippet: membrane-bound electron transport chain
  notes: Review supports proton-gradient energy conservation by prokaryotic respiratory
    chains.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "aerobic respiratory chain"
  reference: PMID:31669488
- taxon_id: NCBITaxon:266
  taxon_label: Paracoccus denitrificans
  note: "mitochondrion-like respiratory chain"
  reference: PMID:9841665
causal_graphs:
- graph_id: aerobic_respiration_terminal_oxidase
  title: Aerobic respiration terminal oxidase mechanism
  description: DOI-backed graph linking oxygen reduction, respiratory electron transport,
    proton motive force, and ATP synthesis.
  nodes:
  - node_id: aerobic_respiration_trait
    label: Aerobic respiration
    node_type: TRAIT
    grounding: METPO:1000801
    description: Oxygen-dependent respiratory energy metabolism.
  - node_id: electron_transport_chain
    label: electron transport chain
    node_type: PATHWAY
    grounding: GO:0022900
    description: Membrane-associated redox chain coupling electron flow to ion translocation.
  - node_id: cytochrome_c_oxidase
    label: cytochrome c oxidase
    node_type: GENE_OR_PROTEIN
    description: Terminal oxidase that transfers electrons to molecular oxygen.
    grounding: UniProtKB:A0A075NZN5
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Terminal electron acceptor in aerobic respiration.
  - node_id: water
    label: water
    node_type: CHEMICAL
    grounding: CHEBI:15377
    description: Reduced product of oxygen reduction.
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical ion gradient generated across the coupling membrane.
    grounding: METPO:1007500
  - node_id: atp_synthase
    label: ATP synthase
    node_type: GENE_OR_PROTEIN
    description: Enzyme complex that uses proton motive force to synthesize ATP.
    grounding: UniProtKB:A0A415TT77
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier produced by oxidative phosphorylation.
  edges:
  - subject: aerobic_respiration_trait
    predicate: has mechanistic pathway
    object: electron_transport_chain
    description: Aerobic respiration uses a membrane-bound respiratory electron transport
      chain.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: membrane-bound electron transport chain
      notes: Review describes respiration as redox reactions catalyzed by membrane-bound
        electron transport chains.
  - subject: cytochrome_c_oxidase
    predicate: reduces
    object: molecular_oxygen
    description: Terminal oxidase transfers electrons to molecular oxygen.
    evidence:
    - reference: DOI:10.1146/annurev.biophys.27.1.329
      snippet: electron transfer from cytochrome c to molecular oxygen
      notes: Supports oxygen as terminal electron acceptor for cytochrome c oxidase.
    predicate_id: METPO:2000017
  - subject: molecular_oxygen
    predicate: reduced to
    object: water
    description: Oxygen reduction forms water at the terminal oxidase.
    evidence:
    - reference: DOI:10.1146/annurev.biophys.27.1.329
      snippet: reducing the latter to water
      notes: Supports water as the product of terminal oxygen reduction.
  - subject: electron_transport_chain
    predicate: generates
    object: proton_motive_force
    description: Respiratory redox energy is conserved as an ion gradient.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: generation of an electrochemical ion gradient
      notes: Supports proton motive force generation by respiratory chains.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: regulates
    object: atp_synthase
    description: The proton motive force powers ATP synthase.
    evidence:
    - reference: DOI:10.1146/annurev.biophys.27.1.329
      snippet: employed by the F0F1-ATPase
      notes: Supports ATP synthase use of the respiratory proton gradient.
    predicate_id: RO:0002211
  - subject: atp_synthase
    predicate: produces
    object: atp
    description: ATP synthase produces ATP during oxidative phosphorylation.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: gradient across a coupling membrane that drives ATP synthesis
      notes: Supports ATP synthesis driven by the respiratory ion gradient.
    predicate_id: METPO:2000202
curation_history:
- timestamp: '2026-05-05T01:35:46.911295+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 oxygen reduction, proton motive force,
    and ATP synthesis in aerobic respiration.
  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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×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: '2026-05-24T04:41:03Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A075NZN5×1, UniProtKB:A0A415TT77×1).
  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: '2026-06-16T06:30:56Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000017×1).
  llm_assisted: true