identifier: METPO:1000656
label: photoautotrophic
definition: A trophic type characterized by the use of light as the energy source
  and carbon dioxide as the primary carbon source for biosynthesis.
definition_source: DOI:10.3390/life10050071
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: anoxygenic_photoautotrophy
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: anoxygenic_photoautotrophy_hydrogen_oxidation
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: anoxygenic_photoautotrophy_iron_oxidation
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: anoxygenic_photoautotrophy_sulfur_oxidation
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: photoautotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: photoautotrophy
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Anthea Guo
evidence:
- reference: DOI:10.3390/life10050071
  snippet: capture solar energy
  notes: Review supports cyanobacterial photoautotrophic use of solar energy and CO2
    fixation.
- reference: DOI:10.1128/AEM.02473-10
  snippet: Calvin-Benson reductive pentose phosphate cycle
  notes: Review supports the Calvin-Benson cycle as a microbial autotrophic CO2-fixation
    pathway.
- reference: PMID:8590279
  snippet: Synechocystis sp. strain PCC6803
  notes: 'Organism example: Synechocystis sp. PCC 6803 is a model photoautotrophic
    cyanobacterium that uses oxygenic photosynthesis to drive Calvin-Benson CO2 fixation
    (Kaneko et al. 1996, DNA Res, full genome).'
canonical_examples:
- taxon_id: NCBITaxon:1148
  taxon_label: Synechocystis sp. PCC 6803
  note: "oxygenic photoautotroph"
  reference: PMID:23945601
- taxon_id: NCBITaxon:1097
  taxon_label: Chlorobaculum tepidum
  note: "anoxygenic photoautotroph"
  reference: PMID:12093901
causal_graphs:
- graph_id: photoautotrophic_cyanobacterial_carbon_fixation
  title: Photoautotrophic light-powered CO2 fixation
  description: DOI-backed graph linking light capture, photosynthetic electron transport,
    ATP/reductant supply, and Calvin-Benson carbon fixation.
  nodes:
  - node_id: photoautotrophic_trait
    label: photoautotrophic
    node_type: TRAIT
    grounding: METPO:1000656
    description: Trophic type using light energy and carbon dioxide for biosynthesis.
  - node_id: light
    label: light
    node_type: ENVIRONMENTAL_FACTOR
    description: Energy source for photoautotrophic metabolism.
    grounding: PATO:0001717
  - node_id: photosystem_ii
    label: photosystem II
    node_type: GENE_OR_PROTEIN
    description: Oxygenic photosystem that extracts electrons from water in cyanobacteria.
  - 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: Product of oxygenic water splitting.
  - node_id: photosynthetic_electron_transport
    label: photosynthetic electron transport
    node_type: PATHWAY
    description: Electron-transfer pathway generating ATP and NADPH.
    grounding: GO:0009767
  - node_id: atp_nadph
    label: ATP and NADPH
    node_type: CHEMICAL
    description: Energy and reductant supply for CO2 assimilation.
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Primary inorganic carbon source.
  - node_id: calvin_benson_cycle
    label: Calvin-Benson cycle
    node_type: PATHWAY
    description: Reductive pentose phosphate CO2-fixation cycle.
    grounding: GO:0019253
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Carboxylating enzyme of the Calvin-Benson cycle.
    grounding: UniProtKB:A0A075WF79
  - node_id: biomass
    label: biomass
    node_type: CHEMICAL
    description: Cellular material formed from fixed carbon.
    grounding: METPO:1007501
  - node_id: carbon_concentrating_mechanism
    label: carbon-concentrating mechanism
    node_type: BIOLOGICAL_PROCESS
    description: Inorganic carbon-concentrating mechanism that elevates CO2 around
      RuBisCO.
  - node_id: rubisco_oxygenase_activity
    label: RuBisCO oxygenase activity
    node_type: MOLECULAR_FUNCTION
    description: Wasteful oxygenation side-reaction of RuBisCO leading to photorespiration.
  - node_id: carboxysome
    label: carboxysome
    node_type: ORGANELLE
    description: Proteinaceous microcompartment housing RuBisCO and carbonic anhydrase
      for CO2 fixation.
    grounding: GO:0031470
  - node_id: carboxysomal_carbonic_anhydrase
    label: carboxysomal carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Carbonic anhydrase that dehydrates bicarbonate to CO2 inside the
      carboxysome.
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    description: Inorganic carbon species accumulated and converted to CO2 for fixation.
    grounding: CHEBI:17544
  edges:
  - subject: photoautotrophic_trait
    predicate: uses energy source
    object: light
    description: Photoautotrophy uses light as the energy source.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: capture solar energy
      notes: Supports light capture by cyanobacteria under photoautotrophic metabolism.
    predicate_id: METPO:2000010
  - subject: photosystem_ii
    predicate: oxidizes
    object: water
    description: Oxygenic photosynthesis extracts electrons from water through PSII.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: uses it to split H2O
      notes: Supports water splitting by PSII in cyanobacteria.
    predicate_id: METPO:2000016
  - subject: water
    predicate: oxidized to
    object: molecular_oxygen
    description: Water oxidation releases molecular oxygen.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: split H2O molecules into O2
      notes: Supports oxygen as the product of water splitting.
    predicate_id: METPO:2007405
  - subject: photosystem_ii
    predicate: feeds electrons into
    object: photosynthetic_electron_transport
    description: PSII feeds electrons into the photosynthetic electron transport chain.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: passes its reducing equivalents to an electron transfer chain
      notes: Supports electron flow from PSII/plastoquinol into photosynthetic electron
        transport.
    predicate_id: METPO:2007402
  - subject: photosynthetic_electron_transport
    predicate: produces
    object: atp_nadph
    description: Photosynthetic electron transport generates ATP and NADPH.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: generate chemical energy (ATP) and reducing power (NADPH)
      notes: Supports ATP and NADPH generation by photosynthetic electron transport.
    predicate_id: METPO:2000202
  - subject: carbon_dioxide
    predicate: fixed by
    object: calvin_benson_cycle
    description: CO2 is assimilated through the Calvin-Benson cycle in many photoautotrophs.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      snippet: Calvin-Benson reductive pentose phosphate cycle
      notes: Supports Calvin-Benson cycle as an autotrophic CO2-fixation route.
    predicate_id: METPO:2007404
  - subject: rubisco
    predicate: catalyzes
    object: calvin_benson_cycle
    description: RuBisCO is a key carboxylating enzyme for Calvin-Benson CO2 fixation.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: Calvin cycle enzymes, RuBisCO
      notes: Supports RuBisCO as a Calvin-cycle enzyme tied to CO2 fixation rate.
    predicate_id: biolink:catalyzes
  - subject: calvin_benson_cycle
    predicate: produces
    object: biomass
    description: Fixed carbon supports biosynthesis and biomass production.
    evidence:
    - reference: DOI:10.3390/life10050071
      snippet: fix ... CO2 into ... biomass
      notes: Supports CO2 fixation into biomass by cyanobacterial photoautotrophy.
    predicate_id: METPO:2000202
  - subject: photosynthetic_electron_transport
    predicate: enables
    object: calvin_benson_cycle
    description: Light-driven photosynthetic electron transport supplies the energy/reductant
      that drives CBB-cycle CO2 fixation.
    evidence:
    - reference: DOI:10.3389/fpls.2024.1417680
      notes: Phototrophs use light energy to drive a photosynthetic electron transport
        chain, and CO2 fixation occurs via the Calvin-Benson-Bassham cycle.
    predicate_id: RO:0002327
  - subject: carbon_concentrating_mechanism
    predicate: lowers
    object: rubisco_oxygenase_activity
    description: The CCM enriches intracellular inorganic carbon, suppressing the
      wasteful RuBisCO oxygenase reaction.
    evidence:
    - reference: DOI:10.3389/fpls.2024.1417680
      notes: The CCM lowers RuBisCO's oxygenase reaction to below ~1% by enriching
        intracellular inorganic carbon.
  - subject: bicarbonate
    predicate: diffuses into
    object: carboxysome
    description: Cytoplasmic bicarbonate enters the carboxysome where it is converted
      to CO2 for fixation.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: Cytoplasmic HCO3- diffuses into the carboxysome.
  - subject: carboxysomal_carbonic_anhydrase
    predicate: converts
    object: bicarbonate
    description: Carboxysomal carbonic anhydrase dehydrates bicarbonate to CO2 to
      feed RuBisCO.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: Bicarbonate is converted back to CO2 by carbonic anhydrase inside carboxysomes
        (CA produces CO2).
curation_history:
- timestamp: '2026-05-05T01:35:46.879777+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 oxygenic light capture, ATP/NADPH generation,
    and Calvin-Benson CO2 fixation.
  llm_assisted: true
- timestamp: '2026-05-16T05:00:00-07:00'
  curator: claude
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Synechocystis sp. PCC 6803 organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×2, METPO:2000010×1, METPO:2000016×1).
  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:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007405×1, METPO:2007402×1, METPO:2007404×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:01Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001717×1, GO:0009767×1, GO:0019253×1).
  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:1007501×1).
  llm_assisted: true
- timestamp: '2026-05-24T07:34:59Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T02:27:52Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A075WF79×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  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: '2026-06-24T17:23:35Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0031470×1, CHEBI:17544×1).
  llm_assisted: true