identifier: METPO:1000060
label: metabolism
definition: A biological process that maintains life in an organism.
definition_source: DOI:10.1126/science.1238842
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000630
created_by: Anthea Guo
evidence:
- reference: DOI:10.1126/science.1238842
  snippet: energy and microbial life
  notes: Microbial-energetics review supports metabolism as the energy and material-flow
    process maintaining microbial life.
- reference: DOI:10.1146/annurev.biochem.71.110601.135503
  snippet: ATP synthesis
  notes: ATP-energetics review supports energy conservation as the central output
    of catabolic metabolism.
causal_graphs:
- graph_id: metabolism_substrate_to_growth
  title: Metabolism substrate-to-growth flow
  description: DOI-backed graph linking substrate uptake, catabolism producing ATP
    and reducing power, biosynthesis, and growth as the core organization of cellular
    metabolism.
  nodes:
  - node_id: metabolism_trait
    label: metabolism
    node_type: TRAIT
    grounding: METPO:1000060
    description: Integrated biological process of substrate, energy, and material
      flow maintaining cellular life.
  - node_id: substrate_uptake
    label: substrate uptake
    node_type: BIOLOGICAL_PROCESS
    description: Transport of carbon, nitrogen, and other substrates into the cell.
  - node_id: catabolism
    label: catabolism
    node_type: BIOLOGICAL_PROCESS
    description: Breakdown of substrates yielding ATP and reducing equivalents.
    grounding: GO:0009056
  - node_id: atp_and_reducing_power
    label: ATP and reducing power
    node_type: CHEMICAL
    description: Energy currency (ATP) and electron carriers (NAD(P)H, FADH2) produced
      by catabolism.
  - node_id: biosynthesis
    label: biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Anabolic synthesis of cellular building blocks and macromolecules.
    grounding: GO:0009058
  - node_id: cellular_growth
    label: cellular growth
    node_type: BIOLOGICAL_PROCESS
    description: Net accumulation of biomass enabling division and survival.
    grounding: GO:0016049
  - node_id: respiratory_electron_transport
    label: respiratory electron transport chain
    node_type: BIOLOGICAL_PROCESS
    description: Membrane electron transfer through respiratory chains that translocates
      protons.
    grounding: GO:0022904
  - node_id: proton_motive_force
    label: proton motive force
    node_type: CHEMICAL
    description: Electrochemical proton gradient across the membrane storing potential
      energy.
  - node_id: atp_synthase
    label: ATP synthase
    node_type: GENE_OR_PROTEIN
    description: Membrane-bound enzyme complex that phosphorylates ADP to ATP using
      the proton motive force.
    grounding: UniProtKB:A0A415TT77
  - node_id: atp_production
    label: ATP production
    node_type: BIOLOGICAL_PROCESS
    description: ATP biosynthetic process generating the cellular energy currency.
  - node_id: respiration_energy_cost
    label: respiration energy demand
    node_type: BIOLOGICAL_PROCESS
    description: Carbon diverted to respiration for energy generation, maintenance,
      and enzyme production.
  - node_id: carbon_use_efficiency
    label: carbon use efficiency
    node_type: QUALITY
    description: Fraction of assimilated carbon converted to biomass rather than respired
      or exuded.
  - node_id: substrate_complexity
    label: substrate complexity
    node_type: QUALITY
    description: Degree to which substrates require enzymatic degradation before uptake.
  - node_id: metabolic_energy_cost
    label: energetic cost of metabolism
    node_type: QUALITY
    description: Energy expenditure required to acquire and process substrates.
  edges:
  - subject: substrate_uptake
    predicate: feeds
    object: catabolism
    description: Imported substrates feed the catabolic reactions of the cell.
    evidence:
    - reference: DOI:10.1126/science.1238842
      snippet: energy and microbial life
      notes: Supports substrate uptake as the input to catabolic energy flow.
  - subject: catabolism
    predicate: produces
    object: atp_and_reducing_power
    description: Catabolic reactions generate ATP and reducing equivalents.
    evidence:
    - reference: DOI:10.1146/annurev.biochem.71.110601.135503
      snippet: ATP synthesis
      notes: Supports ATP and reducing power as canonical outputs of catabolism.
    predicate_id: METPO:2000202
  - subject: atp_and_reducing_power
    predicate: enables
    object: biosynthesis
    description: ATP and reducing power fuel biosynthetic reactions.
    evidence:
    - reference: DOI:10.1146/annurev.biochem.71.110601.135503
      snippet: ATP synthesis
      notes: Supports ATP-driven biosynthesis as the central coupling of energy to
        anabolism.
    predicate_id: RO:0002327
  - subject: biosynthesis
    predicate: enables
    object: cellular_growth
    description: Biosynthesis supports accumulation of biomass and growth.
    evidence:
    - reference: DOI:10.1126/science.1238842
      snippet: energy and microbial life
      notes: Supports biosynthesis-driven growth as the goal of cellular metabolism.
    predicate_id: RO:0002327
  - subject: cellular_growth
    predicate: realizes
    object: metabolism_trait
    description: The coordinated substrate-uptake / catabolism / biosynthesis / growth
      flow realizes the metabolism phenotype.
    evidence:
    - reference: DOI:10.1126/science.1238842
      snippet: energy and microbial life
      notes: Supports metabolism as the integrated process maintaining microbial life.
  - subject: respiratory_electron_transport
    predicate: generates
    object: proton_motive_force
    description: Electron transfer through respiratory chains translocates protons
      to create the gradient.
    evidence:
    - reference: DOI:10.1016/j.heliyon.2023.e22459
      notes: Proton movement driven by respiratory electron transfer creates the gradient
        that powers ATP synthesis.
    predicate_id: biolink:produces
  - subject: atp_synthase
    predicate: uses
    object: proton_motive_force
    description: ATP synthase consumes the electrochemical proton motive force to
      drive phosphorylation.
    evidence:
    - reference: DOI:10.1016/j.heliyon.2023.e22459
      notes: ATP synthase converts ADP + Pi to ATP using an electrochemical proton
        motive force generated by respiratory chains.
  - subject: atp_synthase
    predicate: produces
    object: atp_production
    description: ATP synthase phosphorylates ADP to ATP, generating cellular energy
      currency.
    evidence:
    - reference: DOI:10.1016/j.heliyon.2023.e22459
      notes: Membrane-bound ATP synthase converts potential energy to ATP by phosphorylating
        ADP.
    predicate_id: METPO:2000202
  - subject: respiration_energy_cost
    predicate: decreases
    object: carbon_use_efficiency
    description: Diverting more carbon to respiration lowers the fraction converted
      to biomass.
    evidence:
    - reference: DOI:10.1038/s41467-024-52160-5
      notes: CUE declines when more carbon is diverted to respiration to generate
        energy for uptake, maintenance, and enzyme production.
    predicate_id: RO:0002212
  - subject: substrate_complexity
    predicate: increases
    object: metabolic_energy_cost
    description: Substrates needing enzymatic degradation raise the energetic cost
      of metabolism.
    evidence:
    - reference: DOI:10.1038/s41467-024-52160-5
      notes: Energy required depends on whether compounds are directly taken up or
        need enzymatic degradation.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.810665+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T23:30:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph framing metabolism as the integrated substrate-uptake
    / catabolism / biosynthesis / growth flow that maintains cellular life.
  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: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×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:0002327×1).
  llm_assisted: true
- timestamp: '2026-05-26T05:00:47Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    powers → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0016049×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, METPO:2000202×1, RO:0002212×1, RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:18Z'
  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: '2026-06-24T17:23:32Z'
  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