identifier: traitmech:000021
label: reductive tricarboxylic acid cycle
definition: An autotrophic carbon-fixation pathway (reductive citric acid / Arnon-Buchanan
  cycle) that runs the tricarboxylic acid cycle in reverse to fix CO2. It operates
  in anaerobic and microaerophilic bacteria such as green sulfur bacteria (Chlorobium)
  and Aquificales.
definition_source: DOI:10.1128/AEM.02473-10
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000019
synonyms:
- synonym_text: reductive citric acid cycle
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1128/AEM.02473-10
- synonym_text: rTCA cycle
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/AEM.02473-10
- synonym_text: Arnon-Buchanan cycle
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1146/annurev-marine-120709-142712
evidence:
- reference: DOI:10.1128/AEM.02473-10
  notes: Berg review describes the reductive citric acid cycle as functional in anaerobic/microaerophilic
    autotrophs.
- reference: DOI:10.1146/annurev-marine-120709-142712
  notes: Hügler & Sievert document the rTCA cycle in chemolithoautotrophs and green
    sulfur bacteria in marine systems.
canonical_examples:
- taxon_id: NCBITaxon:1097
  taxon_label: Chlorobaculum tepidum
  note: "Green sulfur bacterium fixing CO2 via the reductive TCA cycle (rTCA first shown in Chlorobia)."
  reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC2998096/
causal_graphs:
- graph_id: rtca_reverse_tricarboxylic_acid_co2_fixation
  title: Reductive TCA cycle runs the TCA cycle in reverse to fix CO2
  description: Evidence-backed causal sketch linking reverse TCA cycle operation in
    anaerobic/microaerophilic autotrophs to CO2 fixation.
  nodes:
  - node_id: rtca_trait
    label: reductive tricarboxylic acid cycle
    node_type: TRAIT
    grounding: traitmech:000021
    description: Autotrophic carbon-fixation pathway running TCA in reverse.
  - node_id: carbon_dioxide
    label: carbon dioxide
    node_type: CHEMICAL
    grounding: CHEBI:16526
    description: Inorganic carbon substrate fixed by the cycle.
  - node_id: citrate
    label: citrate
    node_type: CHEMICAL
    grounding: CHEBI:16947
    description: TCA-cycle intermediate that the reductive cycle generates from CO2.
  - node_id: atp_citrate_lyase
    label: ATP citrate lyase (aclAB)
    node_type: GENE_OR_PROTEIN
    description: Enzyme (EC 2.3.3.8) cleaving citrate into oxaloacetate and acetyl-CoA
      in rTCA.
  - node_id: citryl_coa_synthetase_lyase
    label: citryl-CoA synthetase/lyase route
    node_type: GENE_OR_PROTEIN
    description: Two-enzyme citrate-cleavage system (CCS EC 6.2.1.18 + CCL EC 4.1.3.34)
      alternative to ACL.
  - node_id: pfor
    label: pyruvate:ferredoxin oxidoreductase (PFOR)
    node_type: GENE_OR_PROTEIN
    description: Key rTCA enzyme (EC 1.2.7.1) catalyzing reductive carboxylation of
      acetyl-CoA to pyruvate.
  - node_id: ogor
    label: 2-oxoglutarate:ferredoxin oxidoreductase (OGOR/KOR)
    node_type: GENE_OR_PROTEIN
    description: Key rTCA enzyme (EC 1.2.7.3/1.2.7.11) for reductive carboxylation
      of succinyl-CoA to 2-oxoglutarate.
  - node_id: reduced_ferredoxin
    label: reduced ferredoxin
    node_type: CHEMICAL
    description: Low-potential [4Fe-4S] electron carrier serving as electron donor
      for PFOR and OGOR.
    grounding: CHEBI:17513
  edges:
  - subject: carbon_dioxide
    predicate: fixed by
    object: rtca_trait
    description: CO2 is fixed by the reverse TCA cycle in anaerobic autotrophs.
    evidence:
    - reference: DOI:10.1128/AEM.02473-10
      notes: Berg describes the reductive citric acid cycle as functional in anaerobic/microaerophilic
        autotrophs.
    predicate_id: METPO:2007404
  - subject: rtca_trait
    predicate: produces
    object: citrate
    description: The reverse cycle assembles citrate from CO2.
    evidence:
    - reference: DOI:10.1146/annurev-marine-120709-142712
      notes: Hügler & Sievert document the rTCA cycle in chemolithoautotrophs and
        green sulfur bacteria.
    predicate_id: METPO:2000202
  - subject: atp_citrate_lyase
    predicate: enables
    object: rtca_trait
    description: ATP citrate lyase cleaves citrate into oxaloacetate and acetyl-CoA,
      enabling the rTCA cycle.
    evidence:
    - reference: DOI:10.1101/2022.10.25.513756
      notes: Citrate cleavage into oxaloacetate and acetyl-CoA can be performed by
        ATP-citrate lyase (ACL).
    predicate_id: RO:0002327
  - subject: citryl_coa_synthetase_lyase
    predicate: alternative to
    object: atp_citrate_lyase
    description: The two-enzyme CCS/CCL system is an alternative route to ACL for
      citrate cleavage in rTCA.
    evidence:
    - reference: DOI:10.1101/2022.10.25.513756
      notes: Citrate cleavage can be performed by either a two-enzyme system (CCS/CCL)
        or a single enzyme (ACL).
  - subject: pfor
    predicate: part of
    object: rtca_trait
    description: Pyruvate:ferredoxin oxidoreductase is a canonical key enzyme of the
      rTCA cycle.
    evidence:
    - reference: DOI:10.3390/life13030627
      notes: Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR)
        and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR).
    predicate_id: biolink:part_of
  - subject: ogor
    predicate: part of
    object: rtca_trait
    description: 2-oxoglutarate:ferredoxin oxidoreductase is a canonical key enzyme
      of the rTCA cycle.
    evidence:
    - reference: DOI:10.3390/life13030627
      notes: Key enzymes of this pathway are PFOR and 2-oxoglutarate:ferredoxin oxidoreductase
        (OGOR).
    predicate_id: biolink:part_of
  - subject: reduced_ferredoxin
    predicate: electron donor for
    object: pfor
    description: Reduced low-potential ferredoxin provides electrons to PFOR for reductive
      carboxylation.
    evidence:
    - reference: DOI:10.3390/life13030627
      notes: PFOR and OGOR require a strong reduction potential; Fd6/Fd7 could be
        the physiological electron donors.
  - subject: reduced_ferredoxin
    predicate: electron donor for
    object: ogor
    description: Reduced low-potential ferredoxin provides electrons to OGOR for reductive
      carboxylation.
    evidence:
    - reference: DOI:10.3390/life13030627
      notes: Fd6 and Fd7 can physically interact and exchange electrons with both
        PFOR and OGOR.
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (reductive TCA 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 (rTCA reverse TCA / CO2 fixation) with
    CHEBI node groundings and METPO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 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 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:part_of×2, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17513×1).
  llm_assisted: true