identifier: traitmech:000034
label: oxygenic photosynthesis
definition: A phototrophic metabolism that uses light energy to fix CO2, oxidizing
  water as the electron donor and releasing molecular oxygen. It uses two linked photosystems
  and chlorophyll, and is characteristic of cyanobacteria (and plant chloroplasts).
definition_source: DOI:10.1016/j.tim.2006.09.001
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000038
evidence:
- reference: DOI:10.1016/j.tim.2006.09.001
  notes: Bryant & Frigaard, "Prokaryotic photosynthesis and phototrophy illuminated",
    contrasts oxygenic photosynthesis (water-splitting, O2-evolving) in cyanobacteria
    with anoxygenic phototrophy.
- reference: DOI:10.1146/annurev-earth-060313-054810
  notes: Fischer et al., "Evolution of Oxygenic Photosynthesis", supports water-oxidizing,
    oxygen-evolving photosynthesis as a distinct, cyanobacterial innovation.
canonical_examples:
- taxon_id: NCBITaxon:1148
  taxon_label: Synechocystis sp. PCC 6803
  note: "Default model unicellular cyanobacterium for oxygenic photosynthesis; first phototroph genome-sequenced."
  reference: PMID:16228363
causal_graphs:
- graph_id: oxygenic_photosynthesis_water_splitting
  title: Oxygenic photosynthesis splits water and releases O2
  description: Evidence-backed causal sketch linking two linked photosystems and water
    oxidation to CO2 fixation and oxygen evolution.
  nodes:
  - node_id: oxygenic_photosynthesis_trait
    label: oxygenic photosynthesis
    node_type: TRAIT
    grounding: traitmech:000034
    description: Light-driven CO2 fixation that oxidizes water and evolves O2.
  - node_id: water
    label: water
    node_type: CHEMICAL
    grounding: CHEBI:15377
    description: Electron donor for oxygenic photosynthesis.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: O2 released by water oxidation.
  - node_id: photosynthetic_etc
    label: photosynthetic electron transport
    node_type: PATHWAY
    grounding: GO:0009767
    description: Linked-photosystem electron transport powering CO2 fixation.
  - node_id: photosystem_ii
    label: photosystem II
    node_type: GENE_OR_PROTEIN
    description: Pigment-protein complex that catalyzes light-driven water oxidation.
  - node_id: plastoquinone_pool
    label: plastoquinone/plastoquinol pool
    node_type: CHEMICAL
    description: Mobile quinone electron carrier reduced by PSII (PQ -> PQH2).
  - node_id: cytochrome_b6f
    label: cytochrome b6f complex
    node_type: GENE_OR_PROTEIN
    description: Electron transfer complex linking PSII/plastoquinol to PSI.
  - node_id: photosystem_i
    label: photosystem I
    node_type: GENE_OR_PROTEIN
    description: Pigment-protein complex that oxidizes plastocyanin/cyt c6 and reduces
      ferredoxin.
  - node_id: ferredoxin
    label: ferredoxin
    node_type: GENE_OR_PROTEIN
    description: Iron-sulfur electron carrier reduced by PSI.
    grounding: UniProtKB:A0A009PCQ5
  - node_id: fnr
    label: ferredoxin-NADP+ reductase
    node_type: GENE_OR_PROTEIN
    description: Enzyme reducing NADP+ to NADPH using ferredoxin-derived electrons.
    grounding: UniProtKB:A0A0E2H5I8
  - node_id: nadph
    label: NADPH
    node_type: CHEMICAL
    description: Reducing equivalent generated by the light reactions.
    grounding: CHEBI:16474
  - node_id: proton_motive_force
    label: proton motive force
    node_type: CHEMICAL
    description: Transthylakoid proton motive force generated by linear electron transport.
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    description: Energy currency synthesized by ATP synthase driven by the pmf.
  edges:
  - subject: water
    predicate: oxidized to
    object: molecular_oxygen
    description: Water is the electron donor; its oxidation releases O2.
    evidence:
    - reference: DOI:10.1016/j.tim.2006.09.001
      notes: Bryant & Frigaard contrast oxygenic photosynthesis (water-splitting,
        O2-evolving) with anoxygenic phototrophy.
    predicate_id: METPO:2007405
  - subject: photosynthetic_etc
    predicate: enables
    object: oxygenic_photosynthesis_trait
    description: Two linked photosystems power electron flow from water to NADP+.
    evidence:
    - reference: DOI:10.1146/annurev-earth-060313-054810
      notes: Fischer et al. support water-oxidizing, O2-evolving photosynthesis as
        a cyanobacterial innovation.
    predicate_id: RO:0002327
  - subject: photosystem_ii
    predicate: oxidizes
    object: water
    description: PSII is the primary catalyst of water oxidation in oxygenic photosynthesis.
    evidence:
    - reference: DOI:10.1007/s11120-022-00991-y
      notes: 'Shevela et al. 2023: PSII is the primary catalyst of water oxidation
        in oxygenic photosynthesis.'
    predicate_id: METPO:2000016
  - subject: photosystem_ii
    predicate: reduces
    object: plastoquinone_pool
    description: Electrons extracted from water reduce plastoquinone (PQ -> PQH2).
    evidence:
    - reference: DOI:10.1007/s11120-022-00991-y
      notes: 'Shevela et al. 2023: water oxidation extracts electrons that reduce
        plastoquinone (PQ -> PQH2).'
    predicate_id: METPO:2000017
  - subject: plastoquinone_pool
    predicate: donates electrons to
    object: cytochrome_b6f
    description: Plastoquinol diffuses to reduce the cytochrome b6f complex.
    evidence:
    - reference: DOI:10.3390/plants13152103
      notes: 'Milrad et al. 2024: PQH2 diffuses to reduce the cytochrome b6f complex.'
    predicate_id: METPO:2007403
  - subject: cytochrome_b6f
    predicate: transfers electrons to
    object: photosystem_i
    description: Cyt b6f transfers electrons to PSI via soluble carriers (plastocyanin
      or cytochrome c6).
    evidence:
    - reference: DOI:10.3390/plants13152103
      notes: 'Milrad et al. 2024: electrons transferred from Cytb6f to PSI via plastocyanin
        or cytochrome c6.'
    predicate_id: METPO:2007403
  - subject: photosystem_i
    predicate: reduces
    object: ferredoxin
    description: PSI oxidizes plastocyanin and reduces ferredoxin.
    evidence:
    - reference: DOI:10.1111/1751-7915.14519
      notes: 'Grettenberger et al. 2024: PSI oxidizes plastocyanin and reduces ferredoxin.'
    predicate_id: METPO:2000017
  - subject: fnr
    predicate: reduces
    object: nadph
    description: Ferredoxin-NADP+ reductase reduces NADP+ to NADPH using ferredoxin
      electrons.
    evidence:
    - reference: DOI:10.1111/1751-7915.14519
      notes: 'Grettenberger et al. 2024: electrons via ferredoxin and FNR reduce NADP+
        to NADPH.'
    predicate_id: METPO:2000017
  - subject: photosynthetic_etc
    predicate: generates
    object: proton_motive_force
    description: Linear electron transport generates the transthylakoid proton motive
      force.
    evidence:
    - reference: DOI:10.3390/plants13152103
      notes: 'Milrad et al. 2024: membrane proton motive force produced by these transfers
        comprises dpH and dPsi.'
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives
    object: atp
    description: The proton motive force drives ATP synthesis by ATP synthase.
    evidence:
    - reference: DOI:10.1007/s11120-022-00991-y
      notes: 'Shevela et al. 2023: raised proton motive force drives ATP synthesis
        by ATP synthase.'
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (oxygenic photosynthesis) from literature
    research to fill the phototrophy gap.
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (water-splitting / O2 evolution) with
    CHEBI/GO node groundings and RO/METPO predicate groundings; promoted PROPOSED
    to REVIEWED.
  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: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000017×3, METPO:2007403×2, METPO:2000016×1, biolink:produces×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
    (CHEBI:16474×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:18Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A009PCQ5×1, UniProtKB:A0A0E2H5I8×1).
  llm_assisted: true