identifier: METPO:1000633
label: carboxydotrophic
definition: A trophic type in which an organism derives energy from the oxidation
  of carbon monoxide.
definition_source: DOI:10.1038/nrmicro1595
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
evidence:
- reference: DOI:10.1038/nrmicro1595
  snippet: Carbon monoxide (CO) supports the growth and metabolism
  notes: Review supports aerobic CO oxidation as an energy-supporting metabolism.
- reference: DOI:10.1111/j.1574-6968.1986.tb01858.x
  snippet: presence of the enzyme CO dehydrogenase
  notes: Review supports CODH and CO-insensitive respiratory-chain features in aerobic
    carboxydotrophs.
canonical_examples:
- taxon_id: NCBITaxon:129958
  taxon_label: Carboxydothermus hydrogenoformans
  note: "Thermophilic hydrogenogenic CO oxidiser (CO + H2O -> CO2 + H2). Afipia/Oligotropha carboxidovorans is the aerobic CO-oxidiser model."
  reference: PMID:16311624
causal_graphs:
- graph_id: carboxydotrophic_co_oxidation
  title: Carboxydotrophic carbon monoxide oxidation mechanism
  description: DOI-backed graph linking carbon monoxide, carbon monoxide dehydrogenase,
    respiratory electron transport, and energy conservation.
  nodes:
  - node_id: carboxydotrophic_trait
    label: carboxydotrophic
    node_type: TRAIT
    grounding: METPO:1000633
    description: Trophic type deriving energy from carbon monoxide oxidation.
  - node_id: carbon_monoxide
    label: carbon monoxide
    node_type: CHEMICAL
    grounding: CHEBI:17245
    description: Reduced C1 gas used as an energy substrate.
  - node_id: carbon_monoxide_dehydrogenase
    label: carbon monoxide dehydrogenase
    node_type: GENE_OR_PROTEIN
    description: CODH enzyme oxidizing carbon monoxide.
    grounding: UniProtKB:A0A061JSS8
  - node_id: molybdenum_hydroxylase
    label: molybdenum hydroxylase
    node_type: GENE_OR_PROTEIN
    description: Aerobic CODH enzyme class described for CO oxidizers.
    grounding: UniProtKB:A0A099I9V3
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Oxidized product of CO oxidation.
  - node_id: respiratory_chain
    label: respiratory chain
    node_type: PATHWAY
    description: Electron-transfer system coupled to CO oxidation.
    grounding: GO:0022904
  - node_id: co_insensitive_terminal_oxidase
    label: CO-insensitive terminal oxidase
    node_type: GENE_OR_PROTEIN
    description: Terminal oxidase enabling respiration during CO oxidation.
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Ion gradient used for energy conservation.
    grounding: METPO:1007500
  - node_id: reduced_pyridine_nucleotides
    label: reduced pyridine nucleotides
    node_type: CHEMICAL
    description: Reduced NAD(P)-type carriers generated by reverse electron transfer.
  - node_id: nife_codh
    label: Ni,Fe-carbon monoxide dehydrogenase
    node_type: GENE_OR_PROTEIN
    description: Anaerobic nickel-iron CODH enzyme class.
  - node_id: oxygen_sensitivity
    label: oxygen sensitivity
    node_type: QUALITY
    description: Inactivation/intolerance of an enzyme upon exposure to O2.
  - node_id: oxygen_tolerance
    label: oxygen tolerance
    node_type: QUALITY
    description: Ability of an enzyme to function in the presence of O2.
  - node_id: cox_operon
    label: cox operon
    node_type: GENE_OR_PROTEIN
    description: Operon encoding aerobic Mo-CODH structural subunits coxS, coxM, coxL.
  - node_id: coo_operon
    label: coo operon
    node_type: GENE_OR_PROTEIN
    description: Operon encoding Ni,Fe-CODH and accessory proteins for energy conservation.
  - node_id: cooa_regulator
    label: CooA
    node_type: GENE_OR_PROTEIN
    description: Heme-based CO-sensing transcriptional activator of coo operons.
    grounding: UniProtKB:A0A1D7QXJ2
  - node_id: rcom_regulator
    label: RcoM
    node_type: GENE_OR_PROTEIN
    description: Heme-dependent high-affinity CO sensor regulating aerobic CO oxidation
      genes.
    grounding: UniProtKB:A0A0D5N3T8
  - node_id: atp_synthase
    label: ATP synthase
    node_type: GENE_OR_PROTEIN
    description: Membrane complex synthesizing ATP from an ion motive force.
    grounding: UniProtKB:A0A415TT77
  - node_id: dioxygen
    label: dioxygen
    node_type: CHEMICAL
    description: Terminal electron acceptor in aerobic CO oxidation.
    grounding: CHEBI:15379
  edges:
  - subject: carboxydotrophic_trait
    predicate: uses energy substrate
    object: carbon_monoxide
    description: Carboxydotrophs use carbon monoxide to support growth or metabolism.
    evidence:
    - reference: DOI:10.1038/nrmicro1595
      snippet: CO supports the growth and metabolism
      notes: Supports carbon monoxide as an energy-supporting substrate.
  - subject: carbon_monoxide_dehydrogenase
    predicate: oxidizes
    object: carbon_monoxide
    description: CODH catalyzes carbon monoxide oxidation.
    evidence:
    - reference: DOI:10.1038/nrmicro1595
      snippet: CO dehydrogenase (CODH), to oxidize CO
      notes: Supports CODH-mediated CO oxidation.
    predicate_id: METPO:2000016
  - subject: molybdenum_hydroxylase
    predicate: enzyme class for
    object: carbon_monoxide_dehydrogenase
    description: Aerobic CO oxidizers use a molybdenum hydroxylase CODH.
    evidence:
    - reference: DOI:10.1038/nrmicro1595
      snippet: use a molybdenum hydroxylase
      notes: Supports molybdenum hydroxylase classification of aerobic CODH.
  - subject: carbon_monoxide
    predicate: oxidized to
    object: carbon_dioxide
    description: CO oxidation yields carbon dioxide.
    evidence:
    - reference: DOI:10.1007/s00775-018-1541-0
      snippet: oxidation of CO to CO2
      notes: Supports CO-to-CO2 conversion by CODH.
    predicate_id: METPO:2007405
  - subject: carbon_monoxide_dehydrogenase
    predicate: feeds electrons into
    object: respiratory_chain
    description: CO oxidation is coupled to respiratory electron transfer.
    evidence:
    - reference: DOI:10.1111/j.1574-6968.1986.tb01858.x
      snippet: branched respiratory chain
      notes: Supports respiratory-chain coupling in aerobic CO-utilizing bacteria.
    predicate_id: METPO:2007402
  - subject: respiratory_chain
    predicate: depends on
    object: co_insensitive_terminal_oxidase
    description: CO-utilizing bacteria use a CO-insensitive terminal oxidase branch.
    evidence:
    - reference: DOI:10.1111/j.1574-6968.1986.tb01858.x
      snippet: CO-insensitive terminal oxidase
      notes: Supports terminal oxidase adaptation for CO metabolism.
    predicate_id: RO:0002502
  - subject: respiratory_chain
    predicate: generates
    object: proton_motive_force
    description: Respiratory CO oxidation conserves energy as proton motive force.
    evidence:
    - reference: DOI:10.1111/j.1574-6968.1986.tb01858.x
      snippet: pmf-driven reversed electron transfer
      notes: Supports pmf involvement in aerobic carboxydotrophic energy metabolism.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives formation of
    object: reduced_pyridine_nucleotides
    description: Reverse electron transfer can form reduced pyridine nucleotides.
    evidence:
    - reference: DOI:10.1111/j.1574-6968.1986.tb01858.x
      snippet: formation of reduced pyridine nucleotides
      notes: Supports pmf-driven reverse electron transfer output.
    predicate_id: biolink:produces
  - subject: nife_codh
    predicate: has quality
    object: oxygen_sensitivity
    description: Ni,Fe-CODHs are oxygen sensitive, restricting them to anaerobic carboxydotrophs.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: Ni,Fe-CODHs are noted as oxygen sensitive and associated with anaerobic
        carboxydotrophs.
  - subject: molybdenum_hydroxylase
    predicate: has quality
    object: oxygen_tolerance
    description: Cu,Mo-CODHs are O2-tolerant, enabling aerobic CO metabolism.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: Cu,Mo-CODHs are O2-tolerant (aerobic CO metabolism).
  - subject: cox_operon
    predicate: encodes
    object: molybdenum_hydroxylase
    description: cox operons encode the coxS/coxM/coxL aerobic Mo-CODH subunits.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: Mo-CODH is encoded in cox operons that include coxS, coxM, and coxL.
    predicate_id: biolink:encodes
  - subject: coo_operon
    predicate: encodes
    object: nife_codh
    description: coo operons encode Ni,Fe-CODH plus accessory proteins for energy
      conservation.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: coo operons specifically encode CODH plus accessory proteins for energy
        conservation.
    predicate_id: biolink:encodes
  - subject: cooa_regulator
    predicate: activates transcription of
    object: coo_operon
    description: CO binding to CooA Fe(II)-heme allosterically activates coo operon
      transcription.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: CO binding to Fe(II)-heme allosterically activates promoter binding and
        RNAP recruitment of coo operons.
  - subject: rcom_regulator
    predicate: regulates
    object: cox_operon
    description: RcoM is a high-affinity CO sensor regulating aerobic coxMSL genes.
    evidence:
    - reference: DOI:10.1128/jb.00332-22
      notes: RcoM regulates aerobic CO oxidation and was originally identified upstream
        of coxMSL genes.
    predicate_id: RO:0002211
  - subject: proton_motive_force
    predicate: powers
    object: atp_synthase
    description: The ion motive force generated by CO oxidation drives ATP synthase.
    evidence:
    - reference: DOI:10.1186/s40643-023-00705-9
      notes: Generates an ion motive force that drives ATP synthesis.
  - subject: molybdenum_hydroxylase
    predicate: coupled to reduction of
    object: dioxygen
    description: Mo-CODH-mediated CO oxidation is coupled to O2 reduction aerobically.
    evidence:
    - reference: DOI:10.1101/2023.01.17.524042
      notes: Mo-CODH-mediated CO oxidation supports O2 reduction aerobically.
curation_history:
- timestamp: '2026-05-05T01:35:46.868229+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 CODH-mediated carbon monoxide oxidation,
    respiratory-chain coupling, and energy conservation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000016×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  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: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007405×1, METPO:2007402×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0022904×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  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: '2026-05-24T05:05:15Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A061JSS8×1, UniProtKB:A0A099I9V3×1).
  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: '2026-05-26T05:00:48Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    requires → depends on ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:51Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002502×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:27Z'
  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: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:encodes×2, RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  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: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15379×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1D7QXJ2×1, UniProtKB:A0A0D5N3T8×1).
  llm_assisted: true