identifier: traitmech:000020
label: Calvin-Benson-Bassham cycle
definition: An autotrophic carbon-fixation pathway (the reductive pentose phosphate
  cycle) that fixes CO2 using ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO).
  It is the most widespread CO2-fixation pathway, used by plants, algae, cyanobacteria,
  and many proteobacteria.
definition_source: DOI:10.1128/AEM.02473-10
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000019
synonyms:
- synonym_text: Calvin cycle
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1128/AEM.02473-10
- synonym_text: reductive pentose phosphate cycle
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/AEM.02473-10
evidence:
- reference: DOI:10.1128/AEM.02473-10
  notes: Berg review identifies the Calvin-Benson-Bassham (reductive pentose phosphate)
    cycle as the reference autotrophic pathway against which the other five are distinguished.
- reference: DOI:10.1146/annurev-marine-120709-142712
  notes: Hügler & Sievert support the Calvin cycle as the most common/widespread CO2-fixation
    pathway, including among marine cyanobacteria and proteobacteria.
canonical_examples:
- taxon_id: NCBITaxon:106590
  taxon_label: Cupriavidus necator
  note: "Model chemolithoautotroph fixing CO2 via the Calvin-Benson-Bassham cycle on H2+CO2 (strain H16)."
  reference: PMID:16964242
causal_graphs:
- graph_id: cbb_rubisco_co2_fixation
  title: Calvin-Benson-Bassham cycle fixes CO2 via RuBisCO
  description: Evidence-backed causal sketch linking RuBisCO-catalyzed CO2 carboxylation
    of RuBP to the reductive pentose phosphate cycle.
  nodes:
  - node_id: cbb_trait
    label: Calvin-Benson-Bassham cycle
    node_type: TRAIT
    grounding: traitmech:000020
    description: Reductive pentose phosphate cycle that fixes CO2.
  - node_id: cbb_pathway
    label: Calvin-Benson cycle
    node_type: PATHWAY
    grounding: GO:0019253
    description: Reductive pentose phosphate (Calvin-Benson-Bassham) cycle.
  - node_id: rubisco
    label: RuBisCO
    node_type: GENE_OR_PROTEIN
    description: Ribulose-1,5-bisphosphate carboxylase/oxygenase.
    grounding: UniProtKB:A0A075WF79
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Substrate fixed by RuBisCO.
  - node_id: rubp
    label: ribulose-1,5-bisphosphate
    node_type: CHEMICAL
    description: CO2 acceptor substrate carboxylated by RuBisCO in the CBB cycle.
  - node_id: three_pga
    label: 3-phospho-D-glycerate
    node_type: CHEMICAL
    description: Product of RuBisCO carboxylation of RuBP; first stable CBB intermediate.
    grounding: CHEBI:17794
  - node_id: carboxysome
    label: carboxysome
    node_type: ORGANELLE
    description: Bacterial microcompartment that encapsulates RuBisCO and carbonic
      anhydrase as part of the CO2-concentrating mechanism.
    grounding: GO:0031470
  - node_id: bicarbonate
    label: bicarbonate
    node_type: CHEMICAL
    description: HCO3-, inorganic carbon species converted to CO2 by carbonic anhydrase
      near RuBisCO.
    grounding: CHEBI:17544
  - node_id: carboxysomal_ca
    label: carboxysomal carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Carbonic anhydrase within the carboxysome that converts HCO3- to
      CO2 to supply RuBisCO.
  - node_id: cbbr
    label: CbbR transcriptional regulator
    node_type: GENE_OR_PROTEIN
    description: LysR-type master transcriptional activator of bacterial cbb CO2-fixation
      operons.
  - node_id: cbb_operon
    label: cbb operon
    node_type: GENE_OR_PROTEIN
    description: Operon encoding CBB-cycle CO2-fixation enzymes.
  - node_id: cytoplasmic_ca
    label: cytoplasmic carbonic anhydrase
    node_type: GENE_OR_PROTEIN
    description: Non-vectorial cytosolic carbonic anhydrase whose activity can dissipate
      the CO2-concentrating mechanism.
  - node_id: co2_leakage
    label: CO2 leakage
    node_type: BIOLOGICAL_PROCESS
    description: Dissipation of concentrated CO2 from the CCM, reducing carbon-fixation
      efficiency.
  edges:
  - subject: rubisco
    predicate: enables
    object: cbb_pathway
    description: RuBisCO catalyzes the CO2-fixing carboxylation step of the cycle.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      notes: Berg identifies the CBB cycle as the reference autotrophic pathway.
    predicate_id: RO:0002327
  - subject: cbb_pathway
    predicate: enables
    object: cbb_trait
    description: The reductive pentose phosphate cycle realizes the trait.
    evidence:
    - reference: DOI:10.1146/annurev-marine-120709-142712
      notes: Hügler & Sievert support the Calvin cycle as the most widespread CO2-fixation
        pathway.
    predicate_id: RO:0002327
  - subject: carbon_dioxide
    predicate: fixed by
    object: cbb_trait
    description: CO2 is the substrate fixed by the CBB cycle.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      notes: Berg identifies the CBB cycle as a CO2-fixing pathway.
    predicate_id: METPO:2007404
  - subject: rubisco
    predicate: converts
    object: three_pga
    description: RuBisCO catalyzes the first CBB reaction, carboxylating RuBP with
      CO2 to yield 3-phosphoglycerate.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: 'Kurkela 2024: "RubisCo... catalyses the first CBB reaction (RuBP + CO2
        -> 3-PGA)."'
  - subject: rubp
    predicate: substrate of
    object: rubisco
    description: RuBP is the CO2-acceptor substrate carboxylated by RuBisCO.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: 'Kurkela 2024: RuBP + CO2 -> 3-PGA is the first CBB reaction catalysed
        by RubisCo.'
  - subject: carboxysome
    predicate: contains
    object: rubisco
    description: Carboxysomes encapsulate RuBisCO as part of the CO2-concentrating
      mechanism.
    evidence:
    - reference: DOI:10.1111/ppl.14140
      notes: 'Kurkela 2024: "carboxysomes that encapsulate RuBisCo and carbonic anhydrase."'
  - subject: carboxysome
    predicate: concentrates
    object: carbon_dioxide
    description: Carboxysomes concentrate CO2 near RuBisCO, bridging environmental
      DIC supply to enzymatic demand.
    evidence:
    - reference: DOI:10.1128/AEM.01557-23
      notes: 'Scott 2024: "carboxysomes... concentrate CO2 near Rubisco to bridge
        environmental DIC supply to enzymatic demand."'
  - subject: carboxysomal_ca
    predicate: converts
    object: carbon_dioxide
    description: Carboxysomal carbonic anhydrase converts HCO3- to CO2 to elevate
      luminal CO2 and promote RuBisCO fixation.
    evidence:
    - reference: DOI:10.1126/sciadv.adk7283
      notes: 'Pulsford 2024: within carboxysomes, CA converts HCO3- to CO2 to elevate
        luminal CO2 and promote Rubisco-catalyzed CO2 fixation.'
  - subject: bicarbonate
    predicate: substrate of
    object: carboxysomal_ca
    description: Bicarbonate is dehydrated by carboxysomal carbonic anhydrase to supply
      CO2 to RuBisCO.
    evidence:
    - reference: DOI:10.1126/sciadv.adk7283
      notes: 'Pulsford 2024: carboxysomal CA converts HCO3- to CO2 to promote Rubisco-catalyzed
        CO2 fixation.'
  - subject: cbbr
    predicate: activates transcription of
    object: cbb_operon
    description: CbbR is the master transcriptional activator that elevates expression
      of bacterial cbb CO2-fixation operons.
    evidence:
    - reference: DOI:10.1128/JB.00442-15
      notes: 'Dangel 2015: "CbbR, the Master Regulator for Microbial Carbon Dioxide
        Fixation"; elevates expression of the cbb CO2 fixation operons. Broad evidence
        across bacteria.'
  - subject: cytoplasmic_ca
    predicate: can cause
    object: co2_leakage
    description: Cytosolic (non-vectorial) carbonic anhydrase activity can dissipate
      the CCM by causing CO2 leakage.
    evidence:
    - reference: DOI:10.1128/AEM.01557-23
      notes: 'Scott 2024: "cytosolic (non-vectoral) CA activity can dissipate the
        CCM by causing CO2 leakage."'
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (Calvin-Benson-Bassham carbon-fixation
    cycle); sub-variant of carbon fixation.
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (CBB / RuBisCO CO2 fixation) with CHEBI/GO
    node groundings and RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-14T05:51:45Z'
  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 8 evidence-backed generic edges (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:23:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17794×1, GO:0031470×1, CHEBI:17544×1).
  llm_assisted: true