identifier: METPO:1000650
label: methanotrophic
definition: A trophic type in which an organism uses methane as the primary carbon
  and energy source through oxidation of methane to carbon dioxide.
definition_source: DOI:10.1039/D3CY00737E
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: methanotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Luke Wang
evidence:
- reference: DOI:10.1039/D3CY00737E
  snippet: convert methane to methanol using methane monooxygenase
  notes: Review supports methane monooxygenase as the first aerobic methanotrophy
    step.
canonical_examples:
- taxon_id: NCBITaxon:414
  taxon_label: Methylococcus capsulatus
  note: "Model aerobic methanotroph (gammaproteobacterial; particulate and soluble methane monooxygenase); strain Bath."
  reference: PMID:15383840
causal_graphs:
- graph_id: methanotrophic_methane_oxidation
  title: Aerobic methanotrophic methane oxidation mechanism
  description: DOI-backed graph for aerobic methane oxidation from methane to methanol,
    formaldehyde assimilation, and carbon dioxide production.
  nodes:
  - node_id: methanotrophic_trait
    label: methanotrophic
    node_type: TRAIT
    grounding: METPO:1000650
    description: Trophic type using methane as carbon and energy source.
  - node_id: methane
    label: methane
    node_type: CHEMICAL
    grounding: CHEBI:16183
    description: Primary C1 substrate of methanotrophs.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Oxidant used by aerobic methane monooxygenases.
  - node_id: methane_monooxygenase
    label: methane monooxygenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme family catalyzing the first methane oxidation step.
    grounding: UniProtKB:A0A0A3YNQ7
  - node_id: intracellular_membrane
    label: intracellular membrane
    node_type: CELLULAR_LOCALIZATION
    description: Localization associated with particulate methane monooxygenase.
    grounding: GO:0031090
  - node_id: methanol
    label: methanol
    node_type: CHEMICAL
    grounding: CHEBI:17790
    description: First oxidation product of methane.
  - node_id: methanol_dehydrogenase
    label: methanol dehydrogenase
    node_type: GENE_OR_PROTEIN
    description: Enzyme oxidizing methanol to formaldehyde.
    grounding: UniProtKB:A0A010SCY7
  - node_id: formaldehyde
    label: formaldehyde
    node_type: CHEMICAL
    grounding: CHEBI:16842
    description: Central C1 intermediate for assimilation or oxidation.
  - node_id: formaldehyde_assimilation
    label: formaldehyde assimilation
    node_type: PATHWAY
    description: RuMP or serine pathway incorporation of formaldehyde into biomass.
    grounding: GO:0019649
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Oxidized C1 product of methane metabolism.
  - node_id: copper
    label: copper
    node_type: CHEMICAL
    description: Copper availability acts as a regulatory and cofactor lever in methanotrophy.
  - node_id: particulate_methane_monooxygenase
    label: particulate methane monooxygenase (pMMO)
    node_type: GENE_OR_PROTEIN
    description: Membrane-bound copper-containing methane monooxygenase complex.
  - node_id: soluble_methane_monooxygenase
    label: soluble methane monooxygenase (sMMO)
    node_type: GENE_OR_PROTEIN
    description: Cytoplasmic iron-containing methane monooxygenase, expressed under
      low copper.
  - node_id: pmocab_operon
    label: pmoCAB operon
    node_type: GENE_OR_PROTEIN
    description: Operon encoding the pMMO subunits PmoA, PmoB and PmoC.
  - node_id: pmmo_subunits
    label: PmoA/PmoB/PmoC subunits
    node_type: GENE_OR_PROTEIN
    description: Structural subunits of the particulate methane monooxygenase complex.
  - node_id: mmoxyz_genes
    label: mmoXYZ genes
    node_type: GENE_OR_PROTEIN
    description: Genes encoding the soluble MMO hydroxylase (MMOH) subunits.
  - node_id: mmoh_subunits
    label: MmoX/MmoY/MmoZ (MMOH alpha/beta/gamma)
    node_type: GENE_OR_PROTEIN
    description: Hydroxylase subunits of soluble methane monooxygenase.
  - node_id: methanobactin
    label: methanobactin
    node_type: CHEMICAL
    description: Ribosomally synthesized copper-chelating chalkophore.
    grounding: CHEBI:222862
  - node_id: cuprous_ion
    label: Cu(I)
    node_type: CHEMICAL
    description: Cuprous ion bound with high affinity by methanobactin.
  - node_id: copper_acquisition
    label: copper acquisition
    node_type: BIOLOGICAL_PROCESS
    description: Uptake of copper required for pMMO function.
  edges:
  - subject: methanotrophic_trait
    predicate: uses substrate
    object: methane
    description: Methane is the defining carbon and energy source for methanotrophy.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: methane as carbon and energy sources
      notes: Review places methane among C1 compounds used by methanotrophs.
  - subject: methane_monooxygenase
    predicate: oxidizes
    object: methane
    description: Methane monooxygenase catalyzes methane oxidation.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: methane oxidation ... catalyzed by two types of methane monooxygenases
      notes: Supports MMO as the enzyme for the first oxidation step.
    predicate_id: METPO:2000016
  - subject: methane_monooxygenase
    predicate: uses oxidant
    object: molecular_oxygen
    description: Aerobic methane monooxygenases activate oxygen during methane oxidation.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: activation of molecular oxygen
      notes: Supports oxygen involvement in MMO catalysis.
  - subject: methane
    predicate: oxidized to
    object: methanol
    description: The first aerobic methane oxidation product is methanol.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: convert methane to methanol
      notes: Supports methane-to-methanol conversion by MMO.
    predicate_id: METPO:2007405
  - subject: methane_monooxygenase
    predicate: located in
    object: intracellular_membrane
    description: Particulate methane monooxygenase is membrane associated in methanotrophs.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: pMMO is located in the characteristic intracellular membrane
      notes: Supports subcellular localization for pMMO.
    predicate_id: biolink:located_in
  - subject: methanol_dehydrogenase
    predicate: oxidizes
    object: methanol
    description: Methanol dehydrogenase converts methanol onward to formaldehyde.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: Methanol is oxidized to formaldehyde
      notes: Supports methanol dehydrogenase as the next step.
    predicate_id: METPO:2000016
  - subject: formaldehyde
    predicate: participates in
    object: formaldehyde_assimilation
    description: Formaldehyde can be assimilated through RuMP or serine pathways.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: RuMP pathway and the serine pathway
      notes: Supports formaldehyde assimilation routes in methanotrophs.
    predicate_id: biolink:participates_in
  - subject: methanotrophic_trait
    predicate: produces
    object: carbon_dioxide
    description: Methane oxidation can continue to carbon dioxide for energy metabolism.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      snippet: methane cycle between ... methane and CO2
      notes: Supports methane oxidation in the methane-carbon dioxide cycle; graph
        focuses on aerobic methanotrophy.
    predicate_id: METPO:2000202
  - subject: copper
    predicate: positively regulates
    object: particulate_methane_monooxygenase
    description: High copper favors pMMO expression (the copper switch).
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      notes: high copper favors pMMO and represses sMMO
  - subject: copper
    predicate: negatively regulates
    object: soluble_methane_monooxygenase
    description: High copper represses sMMO; low copper favors sMMO (the copper switch).
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      notes: high copper favors pMMO and represses sMMO; low copper/biomass favors
        sMMO
  - subject: pmocab_operon
    predicate: encodes
    object: pmmo_subunits
    description: pmoCAB operon encodes the PmoA, PmoB and PmoC subunits of pMMO.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      notes: pMMO ... composed of subunits PmoA, PmoB, and PmoC, encoded by the pmoCAB
        operon
    predicate_id: biolink:encodes
  - subject: mmoxyz_genes
    predicate: encodes
    object: mmoh_subunits
    description: mmoXYZ genes encode the MMOH alpha/beta/gamma hydroxylase subunits
      of sMMO.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      notes: MMOH is a dimer of heterotrimers encoded by the mmoXYZ genes
    predicate_id: biolink:encodes
  - subject: methanobactin
    predicate: binds
    object: cuprous_ion
    description: Methanobactin binds Cu(I) with high affinity.
    evidence:
    - reference: DOI:10.1021/acs.chemrev.3c00727
      notes: Mbns are ribosomally synthesized ... that bind Cu(I) with particularly
        high affinity
  - subject: methanobactin
    predicate: enables
    object: copper_acquisition
    description: Methanobactin-mediated copper chelation enables copper uptake.
    evidence:
    - reference: DOI:10.1039/D3CY00737E
      notes: some methanotrophs produce methanobactin (high affinity for Cu(I)) for
        copper collection
    predicate_id: RO:0002327
  - subject: copper_acquisition
    predicate: promotes
    object: particulate_methane_monooxygenase
    description: Copper acquisition supplies the cofactor required for pMMO activity.
    evidence:
    - reference: DOI:10.1021/acs.chemrev.3c00727
      notes: As a required cofactor for pMMO activity ... copper is central to methanotroph
        physiology
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.876493+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 aerobic methane oxidation by methane
    monooxygenase and downstream C1 metabolism.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000016×2, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-20T05:49:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:located_in×1).
  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:2007405×1).
  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:A0A0A3YNQ7×1, UniProtKB:A0A010SCY7×1).
  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:
    input to → participates in ×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
    (biolink:participates_in×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:47Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0019649×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (10 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:encodes×2, RO:0002327×1, RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0031090×1, CHEBI:222862×1).
  llm_assisted: true