identifier: traitmech:000067 label: polyhydroxyalkanoate granule definition: An intracellular storage inclusion composed of polyhydroxyalkanoate (e.g. polyhydroxybutyrate, PHB), a carbon and energy reserve accumulated as cytoplasmic granules. definition_source: DOI:10.1128/mr.54.4.450-472.1990 trait_category: MORPHOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000066 synonyms: - synonym_text: PHB granule synonym_type: RELATED_SYNONYM source: DOI:10.1128/mr.54.4.450-472.1990 - synonym_text: polyhydroxybutyrate inclusion synonym_type: RELATED_SYNONYM source: DOI:10.1128/mr.54.4.450-472.1990 evidence: - reference: DOI:10.1128/mr.54.4.450-472.1990 notes: Anderson & Dawes describe polyhydroxyalkanoates (chiefly PHB) as carbon/energy reserves stored as cytoplasmic granules. - reference: DOI:10.1038/s41579-020-0413-0 notes: Greening & Lithgow include storage granules such as PHA bodies among bacterial intracellular organelles. canonical_examples: - taxon_id: NCBITaxon:106590 taxon_label: Cupriavidus necator note: "Model PHA/PHB accumulator (strain H16; formerly Ralstonia eutropha / Alcaligenes eutrophus)." reference: PMID:16964242 causal_graphs: - graph_id: pha_granule_carbon_energy_storage title: PHA granules store carbon and energy as polyhydroxyalkanoate description: Evidence-backed causal sketch linking polyhydroxyalkanoate biosynthesis to intracellular storage granules serving as carbon and energy reserves. nodes: - node_id: pha_granule_trait label: polyhydroxyalkanoate granule node_type: TRAIT grounding: traitmech:000067 description: Cytoplasmic granule composed of polyhydroxyalkanoate (e.g. PHB). - node_id: polyhydroxyalkanoate label: polyhydroxyalkanoate node_type: CHEMICAL description: Polyester carbon/energy storage polymer (chiefly PHB). - node_id: carbon_energy_storage label: carbon and energy storage node_type: BIOLOGICAL_PROCESS description: Accumulation of carbon/energy reserves under nutrient excess. - node_id: nutrient_limitation_high_cn label: nutrient limitation / high C:N ratio node_type: ENVIRONMENTAL_FACTOR description: High carbon-to-nitrogen ratio and depletion of N, S, or P with excess carbon. - node_id: pha_accumulation label: polyhydroxyalkanoate accumulation node_type: BIOLOGICAL_PROCESS description: Intracellular accumulation of PHA/PHB polymer. - node_id: pha_synthase_phac label: PHA synthase (PhaC) node_type: GENE_OR_PROTEIN description: Polymerase that condenses (R)-3-hydroxyacyl-CoA into PHA/PHB polymer. - node_id: phasin_phap label: phasin (PhaP) node_type: GENE_OR_PROTEIN description: Granule-associated protein coating and stabilizing PHB chains at the granule surface. - node_id: phb_granule_size_number label: PHB granule size and number node_type: QUALITY description: Morphological quality of granule dimensions and count per cell. - node_id: phar_regulator label: PhaR regulator node_type: GENE_OR_PROTEIN description: Transcriptional repressor that binds phaP promoters. - node_id: phap_gene label: phaP gene node_type: GENE_OR_PROTEIN description: Gene encoding phasin. - node_id: pha_depolymerase_phaz label: PHA depolymerase (PhaZ) node_type: GENE_OR_PROTEIN description: Intracellular depolymerase cleaving PHB to 3-hydroxybutyrate. - node_id: phb_mobilization label: PHB mobilization node_type: BIOLOGICAL_PROCESS description: Degradation and utilization of stored PHB as carbon/energy reserve. - node_id: carbon_starvation label: carbon starvation node_type: ENVIRONMENTAL_FACTOR description: Starvation or exogenous carbon depletion. - node_id: phb_degradation label: PHB degradation node_type: BIOLOGICAL_PROCESS description: Breakdown of stored PHB polymer. edges: - subject: polyhydroxyalkanoate predicate: located in object: pha_granule_trait description: PHA polymer accumulates inside cytoplasmic granules. evidence: - reference: DOI:10.1128/mr.54.4.450-472.1990 notes: Anderson & Dawes describe PHAs (chiefly PHB) as carbon/energy reserves stored as cytoplasmic granules. predicate_id: biolink:located_in - subject: pha_granule_trait predicate: enables object: carbon_energy_storage description: PHA granules realize the carbon/energy storage function. evidence: - reference: DOI:10.1038/s41579-020-0413-0 notes: Greening & Lithgow include PHA bodies among bacterial intracellular organelles. predicate_id: RO:0002327 - subject: nutrient_limitation_high_cn predicate: increases object: pha_accumulation description: High C/N ratio and N/S/P depletion stimulate PHA accumulation. evidence: - reference: DOI:10.3390/molecules29102293 notes: PHA accumulation is stimulated by a high C/N ratio, depletion of N, S, and P, or a low rate of respiration. predicate_id: RO:0002213 - subject: nutrient_limitation_high_cn predicate: induces object: pha_accumulation description: Nutrient limitation with excess carbon induces PHA accumulation. evidence: - reference: DOI:10.1016/j.jbc.2024.107523 notes: Environmental triggers include nutrient limitation and excess carbon that induce PHA accumulation. - subject: pha_synthase_phac predicate: catalyzes object: polyhydroxyalkanoate description: PhaC polymerizes hydroxyacyl-CoA into PHA/PHB polymer. evidence: - reference: DOI:10.3390/polym15143027 notes: PhbC polymerizing beta-hydroxybutyryl-CoA into PHB. predicate_id: biolink:catalyzes - subject: phasin_phap predicate: stabilizes object: polyhydroxyalkanoate description: Phasins coat and stabilize PHB chains at the granule surface. evidence: - reference: DOI:10.3390/polym15143027 notes: Phasins are GAPs that coat and stabilize PHB chains. - subject: phasin_phap predicate: controls object: phb_granule_size_number description: Phasins control the size and number of PHB granules. evidence: - reference: DOI:10.3390/polym15143027 notes: Phasins control the size of the PHB granules. predicate_id: RO:0002211 - subject: phar_regulator predicate: represses transcription of object: phap_gene description: PhaR binds phaP promoters and represses transcription. evidence: - reference: DOI:10.1016/j.jbc.2024.107523 notes: PhaR is a transcriptional repressor that binds phaP promoters and represses their transcription. - subject: pha_depolymerase_phaz predicate: mediates object: phb_mobilization description: PHB depolymerase cleaves PHB to 3-hydroxybutyrate, mediating mobilization. evidence: - reference: DOI:10.3390/polym15143027 notes: PHB mobilization involves a PHB depolymerase (PhbZ/PhaZ) that cleaves PHB to beta-hydroxybutyrate. - subject: carbon_starvation predicate: triggers object: phb_degradation description: Starvation or exogenous carbon depletion triggers PHB degradation. evidence: - reference: DOI:10.3390/polym15143027 notes: PHB is degraded during starvation/exogenous carbon depletion or stationary phase. curation_history: - timestamp: '2026-06-03T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate MORPHOLOGY trait (polyhydroxyalkanoate/PHB granule); storage 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 (PHA granule carbon/energy storage) with RO/biolink 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 (11 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:13Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1, biolink:catalyzes×1, RO:0002211×1). llm_assisted: true