identifier: traitmech:000072 label: carboxysome definition: A bacterial microcompartment — a polyhedral protein-shelled organelle that encapsulates RuBisCO and carbonic anhydrase to concentrate CO2 for carbon fixation in cyanobacteria and many chemoautotrophs. definition_source: DOI:10.1038/nrmicro.2018.10 trait_category: MORPHOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000066 synonyms: - synonym_text: bacterial microcompartment synonym_type: RELATED_SYNONYM source: DOI:10.1038/nrmicro.2018.10 evidence: - reference: DOI:10.1038/nrmicro.2018.10 notes: Kerfeld et al. review bacterial microcompartments; the carboxysome is the archetypal protein-shelled CO2-fixing microcompartment. - reference: DOI:10.1038/nrmicro1913 notes: Yeates et al. describe protein-based organelles in bacteria (carboxysomes and related microcompartments), including the carboxysome shell and its encapsulated enzymes. canonical_examples: - taxon_id: NCBITaxon:32046 taxon_label: Synechococcus elongatus note: "Model for beta-carboxysomes (cyanobacterial CO2-fixing microcompartments; strain PCC 7942). Halothiobacillus neapolitanus is the alpha-carboxysome model." reference: DOI:10.1128/mmbr.00061-12 causal_graphs: - graph_id: carboxysome_co2_concentrating title: Carboxysome encapsulates RuBisCO to concentrate CO2 for carbon fixation description: Evidence-backed causal sketch linking the carboxysome protein shell encapsulating RuBisCO and carbonic anhydrase to enhanced carbon fixation. nodes: - node_id: carboxysome_trait label: carboxysome node_type: TRAIT grounding: traitmech:000072 description: Polyhedral protein-shelled microcompartment encapsulating RuBisCO. - node_id: bacterial_microcompartment label: bacterial microcompartment node_type: CELLULAR_LOCALIZATION grounding: GO:0031469 description: Protein-shelled prokaryotic microcompartment organelle. - node_id: carbon_fixation label: carbon fixation node_type: BIOLOGICAL_PROCESS grounding: GO:0015977 description: Conversion of inorganic CO2 into organic carbon (Calvin cycle). - node_id: carbon_dioxide label: carbon dioxide node_type: CHEMICAL grounding: CHEBI:16526 description: CO2 substrate concentrated by the carboxysome shell. - node_id: carboxysome_shell label: carboxysome shell node_type: ORGANELLE description: Polyhedral selectively permeable protein shell of the carboxysome. - node_id: carbonic_anhydrase label: carbonic anhydrase node_type: GENE_OR_PROTEIN description: Carboxysomal enzyme dehydrating bicarbonate to CO2 near RuBisCO. grounding: UniProtKB:A0A009PMS8 - node_id: bicarbonate label: bicarbonate node_type: CHEMICAL description: HCO3- accumulated in cytoplasm and imported into the carboxysome. grounding: CHEBI:17544 - node_id: oxygen label: oxygen node_type: CHEMICAL description: O2; competing substrate of RuBisCO whose influx the shell limits. - node_id: rubisco_carboxylation label: RuBisCO carboxylation node_type: MOLECULAR_FUNCTION description: Carboxylation of RuBP by RuBisCO, the productive carbon-fixation reaction. - node_id: bmc_shell_proteins label: BMC-H/T/P shell proteins node_type: GENE_OR_PROTEIN description: Hexameric, trimeric and pentameric protein paralogues forming the BMC shell. edges: - subject: carboxysome_trait predicate: example of object: bacterial_microcompartment description: The carboxysome is the archetypal bacterial microcompartment. evidence: - reference: DOI:10.1038/nrmicro1913 notes: Yeates et al. describe the carboxysome shell and its encapsulated enzymes. predicate_id: rdfs:subClassOf - subject: carboxysome_trait predicate: contributes to object: carbon_fixation description: Carboxysomal CO2 concentration accelerates RuBisCO-catalysed fixation. evidence: - reference: DOI:10.1038/nrmicro.2018.10 notes: Kerfeld et al. frame the carboxysome as a CO2-concentrating microcompartment supporting carbon fixation. predicate_id: RO:0002326 - subject: carbon_dioxide predicate: located in object: carboxysome_trait description: CO2 is concentrated within the carboxysome shell for fixation. evidence: - reference: DOI:10.1038/nrmicro.2018.10 notes: Kerfeld et al. review CO2 concentration inside the carboxysome. predicate_id: biolink:located_in - subject: carboxysome_shell predicate: prevents loss of object: carbon_dioxide description: The carboxysome protein shell retains CO2, preventing its escape to the cytoplasm. evidence: - reference: DOI:10.1038/nrmicro.2018.10 notes: 'Kerfeld 2018: "The shell prevents loss of CO2 to the cytoplasm."' - subject: carbonic_anhydrase predicate: converts object: bicarbonate description: Carboxysomal carbonic anhydrase dehydrates imported bicarbonate to CO2. evidence: - reference: DOI:10.1128/aem.01075-24 notes: 'Wieschollek 2024: HCO3- entering carboxysomes is converted by CA to CO2; broad to bacterial CCMs with carboxysomes.' - subject: carboxysome_shell predicate: permits passage of object: bicarbonate description: Selective shell permeability allows HCO3- (and RuBP) to enter the carboxysome. evidence: - reference: DOI:10.1093/plphys/kiae438 notes: 'Cheng 2024: "the shell has selective permeability that permits HCO3- and RuBP passage."' - subject: carboxysome_shell predicate: limits influx of object: oxygen description: The carboxysome shell restricts O2 influx, reducing unproductive RuBisCO oxygenation. evidence: - reference: DOI:10.1093/plphys/kiae438 notes: 'Cheng 2024: shell permits HCO3-/RuBP passage "while limiting O2 influx."' - subject: carbonic_anhydrase predicate: elevates local concentration of object: carbon_dioxide description: CA activity inside the carboxysome elevates local CO2 around RuBisCO. evidence: - reference: DOI:10.1093/plphys/kiae438 notes: 'Cheng 2024: "CA inside the carboxysome dehydrates HCO3- to CO2, elevating CO2 concentration around Rubisco."' - subject: carbon_dioxide predicate: enhances object: rubisco_carboxylation description: Elevated CO2 around RuBisCO enhances carboxylation and reduces oxygenation. evidence: - reference: DOI:10.1093/plphys/kiae438 notes: 'Cheng 2024: elevated CO2 "enhances Rubisco carboxylation rates and reduces unproductive oxygenation."' - subject: bmc_shell_proteins predicate: form object: carboxysome_shell description: BMC-H hexamers, BMC-T pseudohexamers and BMC-P pentamers form the selectively permeable shell with central pores. evidence: - reference: DOI:10.1038/nrmicro.2018.10 notes: 'Kerfeld 2018: BMC-H/T/P proteins build the shell; a central pore "serves as a channel for metabolites"; generalized across BMCs including carboxysomes.' curation_history: - timestamp: '2026-06-03T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate MORPHOLOGY trait (carboxysome); protein-microcompartment sub-variant of intracellular inclusion. llm_assisted: true - timestamp: '2026-06-09T15:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (carboxysome CO2-concentrating / carbon fixation) with GO/CHEBI node groundings and RO/RDFS/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report. 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:17544×1). llm_assisted: true - timestamp: '2026-06-26T07:15:19Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A009PMS8×1). llm_assisted: true