identifier: traitmech:000036
label: proteorhodopsin phototrophy
definition: A light-harvesting metabolism in which a retinal-containing membrane protein
  (proteorhodopsin) acts as a light-driven proton pump, generating proton motive force
  without chlorophyll-based reaction centers. Widespread among marine bacterioplankton.
definition_source: DOI:10.1126/science.289.5486.1902
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000037
synonyms:
- synonym_text: rhodopsin-based phototrophy
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/35081051
evidence:
- reference: DOI:10.1126/science.289.5486.1902
  notes: Béjà et al. identified proteorhodopsin, a retinal-binding light-driven proton
    pump in an uncultivated marine bacterium, as evidence for a new type of phototrophy
    in the sea.
- reference: DOI:10.1038/35081051
  notes: Béjà et al., "Proteorhodopsin phototrophy in the ocean", supports proteorhodopsin
    as a widespread, spectrally tuned light-energy capture system in marine bacteria.
canonical_examples:
- taxon_id: NCBITaxon:313590
  taxon_label: Dokdonia sp. MED134
  note: "Canonical proteorhodopsin phototroph: light stimulates growth under oligotrophic conditions (retinal-inhibition causally proven). Ca. Pelagibacter ubique uses PR for starvation maintenance."
  reference: PMID:17215843
causal_graphs:
- graph_id: proteorhodopsin_light_driven_proton_pump
  title: Proteorhodopsin pumps protons under illumination, generating PMF
  description: Evidence-backed causal sketch linking retinal-based proteorhodopsin
    light-driven proton pumping to proton motive force without chlorophyll-based reaction
    centers.
  nodes:
  - node_id: proteorhodopsin_trait
    label: proteorhodopsin phototrophy
    node_type: TRAIT
    grounding: traitmech:000036
    description: Retinal-based light-driven proton-pumping phototrophy.
  - node_id: proteorhodopsin
    label: proteorhodopsin
    node_type: GENE_OR_PROTEIN
    description: Retinal-binding light-driven proton pump.
    grounding: UniProtKB:A0A1D7QWW9
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    grounding: METPO:1007500
    description: Transmembrane proton gradient generated by light-driven pumping.
  - node_id: proton_pumping
    label: light-driven proton pumping
    node_type: BIOLOGICAL_PROCESS
    description: Proteorhodopsin-mediated transmembrane proton transport driven by
      light.
  - node_id: atp_production
    label: ATP production
    node_type: BIOLOGICAL_PROCESS
    description: ATP biosynthesis driven by PMF generated by proteorhodopsin proton
      pumping.
  - node_id: nadph
    label: NAD(P)H
    node_type: CHEMICAL
    description: Reducing equivalents for anabolic metabolism, not generated by proteorhodopsin.
    grounding: CHEBI:13392
  - node_id: all_trans_retinal
    label: all-trans retinal
    node_type: CHEMICAL
    description: Chromophore cofactor that forms a Schiff base with a central lysine
      in proteorhodopsin.
  - node_id: beta_carotene
    label: beta-carotene
    node_type: CHEMICAL
    description: Carotenoid precursor cleaved by dioxygenase to yield retinal.
    grounding: CHEBI:17579
  edges:
  - subject: proteorhodopsin
    predicate: enables
    object: proteorhodopsin_trait
    description: The retinal-binding pump realizes proteorhodopsin phototrophy.
    evidence:
    - reference: DOI:10.1126/science.289.5486.1902
      notes: Béjà et al. identified proteorhodopsin as a retinal-binding light-driven
        proton pump.
    predicate_id: RO:0002327
  - subject: proteorhodopsin_trait
    predicate: enables
    object: proton_motive_force
    description: Light-driven proton pumping by proteorhodopsin generates PMF.
    evidence:
    - reference: DOI:10.1038/35081051
      notes: Béjà et al. support proteorhodopsin as a widespread light-energy capture
        system in marine bacteria.
    predicate_id: RO:0002327
  - subject: proton_pumping
    predicate: generates
    object: proton_motive_force
    description: Light-driven proton pumping by proteorhodopsin drives PMF generation.
    evidence:
    - reference: DOI:10.4014/jmb.2410.10034
      notes: 'Oh 2024: "PR drives PMF generation".'
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: enables
    object: atp_production
    description: PR-mediated proton transport generates a membrane potential sufficient
      for ATP production.
    evidence:
    - reference: DOI:10.1007/s12275-024-00125-0
      notes: 'Lee 2024: "PR-mediated proton transport could generate a sufficient
        membrane potential for ATP production".'
    predicate_id: RO:0002327
  - subject: proteorhodopsin_trait
    predicate: does not produce
    object: nadph
    description: Proteorhodopsin phototrophy cannot generate NAD(P)H for anabolic
      metabolism; ATP-only energy module.
    evidence:
    - reference: DOI:10.4014/jmb.2410.10034
      notes: 'Oh 2024: "PR can never be harnessed to generate NAD(P)H for anabolic
        metabolism".'
    predicate_id: METPO:2000222
  - subject: all_trans_retinal
    predicate: required for
    object: proteorhodopsin
    description: Functional proteorhodopsin requires all-trans retinal bound via a
      Schiff base to a central lysine.
    evidence:
    - reference: DOI:10.1038/s41467-024-50960-3
      notes: 'Hirschi 2024: "Functional proteorhodopsin requires insertion of all-trans
        retinal by formation of a Schiff base with a central lysine".'
  - subject: beta_carotene
    predicate: cleaved to produce
    object: all_trans_retinal
    description: Beta-carotene is cleaved by dioxygenase into retinal, an essential
      element of functional PR.
    evidence:
    - reference: DOI:10.34133/2022/9782712
      notes: 'Jing 2022: "beta-carotene can be cleaved by dioxygenase into retinal,
        which is an important element in functional PR".'
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (proteorhodopsin phototrophy) from
    literature research to fill the light-driven-energy gap.
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (proteorhodopsin light-driven proton
    pump) with METPO node grounding and RO predicate groundings; promoted PROPOSED
    to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-14T06:38:15Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1D7QWW9×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:13392×1, CHEBI:17579×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:38Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000222×1).
  llm_assisted: true