identifier: traitmech:000673 label: cyanophycin granule definition: An intracellular storage inclusion composed of cyanophycin, a nonribosomal arginine- and aspartate-rich polymer serving as a nitrogen reserve. definition_source: DOI:10.1128/AEM.01298-18 trait_category: MORPHOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000066 evidence: - reference: DOI:10.1007/s002030100281 snippet: Cyanophycin granules reached a maximum after the peak of nitrogenase activity and eventually were utilized completely. notes: Li et al. (2001), publisher scientific abstract directly read at https://link.springer.com/article/10.1007/s002030100281. Electron microscopy and biochemistry identified granules in Cyanothece ATCC 51142 during nitrogen-fixing growth on a 12-hour light/12-hour dark cycle. Full text and figures were not accessible; timing is condition-specific, not a universal granule property. The separate PCC 6803 mutant observations do not establish a universal cyanophycinase requirement. canonical_examples: - taxon_id: NCBITaxon:43989 taxon_label: Crocosphaera subtropica ATCC 51142 reference: DOI:10.1007/s002030100281 note: 'Historical Cyanothece ATCC 51142: granules observed during nitrogen-fixing light/dark culture, not constitutively in every cell. NCBI directly confirms the current strain name, rank no rank, and BH68/BH68K synonym: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=43989. The directly read scientific abstract of the original isolation paper, https://doi.org/10.1128/jb.175.5.1284-1292.1993, places BH68 in intertidal sands of the Texas Gulf coast. This is provenance support, not an independent cyanophycin assay.' causal_graphs: - graph_id: cyanophycin_synthesis_and_storage title: CphA supplies polymer for cyanophycin storage granules scope_status: MECHANISTIC description: A source-bounded synthesis, material-localization and nitrogen-storage sketch, not a claim that every inclusion shares one regulation. scope_notes: Integrates PCC 6308 enzyme expression/purification with PCC 6803 cell biology. It is not one experiment or a strain-specific mechanism demonstrated in the ATCC 51142 canonical example. The sequence-family match establishes identity, not granule formation. No universal growth benefit, magnesium dependence in vivo, degradation enzyme, or granule-surface organizer is inferred. nodes: - node_id: cyanophycin_synthetase_cpha label: cyanophycin synthetase CphA node_type: GENE_OR_PROTEIN grounding: InterPro:IPR011810 gene_symbols: - cphA description: Cyanophycin synthetase family, verified at the InterPro authority; not an isolated ATP-grasp domain. protein_examples: - uniprot_id: UniProtKB:P56947 protein_label: Cyanophycin synthetase gene_symbol: cphA taxon_id: NCBITaxon:113355 taxon_label: Geminocystis herdmanii PCC 6308 entry_status: REVIEWED retrieved_on: '2026-10-08' entry_version: 91 sequence_version: 2 role: PCC 6308 enzyme catalyzes cyanophycin synthesis; functional expression and purification used recombinant E. coli, not a natural E. coli phenotype. evidence: - reference: DOI:10.1007/s002030000206 snippet: The functionality of cphA was proven by heterologous expression of active enzyme and synthesis of cyanophycin in Escherichia coli notes: Aboulmagd et al. (2000), scientific abstract directly read in DOI-matched Europe PMC core metadata (PMID:11131019); full paper not inspected. UniProt REST P56947 links this paper and AF220099/AAF43647.2 to PCC 6308; its entry version 91, sequence version 2 and NCBITaxon:113355 were checked live. The paper's Synechocystis name is historical. The accession is not PCC 6803 or the heterologous expression host. - node_id: cyanophycin_synthesis label: cyanophycin synthesis node_type: BIOLOGICAL_PROCESS description: Nonribosomal polymer synthesis from arginine and aspartate. - node_id: cyanophycin_macromolecule label: cyanophycin macromolecule node_type: CHEMICAL grounding: CHEBI:65318 description: Authority-verified aspartate-backbone, arginine-side-group polymer; chemical identity is not the granule phenotype. - node_id: cyanophycin_granule_trait label: cyanophycin granule node_type: TRAIT grounding: traitmech:000673 - node_id: temporary_nitrogen_storage label: temporary nitrogen storage node_type: BIOLOGICAL_PROCESS description: Retention of assimilated nitrogen for subsequent utilization. edges: - subject: cyanophycin_synthetase_cpha predicate: enables predicate_id: RO:0002327 object: cyanophycin_synthesis description: Purified PCC 6308 CphA catalyzes polymer synthesis. evidence: - reference: DOI:10.1128/AEM.67.5.2176-2182.2001 snippet: which catalyzed the incorporation of arginine and aspartic acid into cyanophycin notes: 'Aboulmagd et al. (2001), scientific abstract: the quoted relative clause describes the native enzyme purified from recombinant E. coli. Publisher full-text Methods and substrate/primer Results were read, including Tables 2 and 3. No actual figure images were inspected.' - subject: cyanophycin_synthesis predicate: has output predicate_id: RO:0002234 object: cyanophycin_macromolecule description: The assayed reaction incorporates amino acids into cyanophycin. evidence: - reference: DOI:10.1128/AEM.67.5.2176-2182.2001 snippet: which catalyzed the incorporation of arginine and aspartic acid into cyanophycin notes: Same abstract clause supports the product as well as catalysis. Radiometric incorporation into insoluble polymer is the assay readout. This does not equate soluble synthesis or engineered amino-acid variants with a cellular granule. - subject: cyanophycin_macromolecule predicate: located in predicate_id: biolink:located_in object: cyanophycin_granule_trait description: Accumulated cyanophycin forms the material of the inclusion. evidence: - reference: DOI:10.1128/AEM.01298-18 snippet: Cyanophycin accumulates in the form of opaque and light-scattering granules in the cell notes: Watzer and Forchhammer (2018), Introduction, directly read in publisher HTML. Results report microscopy and arginine-specific Sakaguchi staining during nitrogen resuscitation in the engineered PCC 6803 CphA-eGFP strain. Main text, Methods and supplemental captions were read; actual figure images were not inspected. - subject: cyanophycin_granule_trait predicate: contributes to predicate_id: RO:0002326 object: temporary_nitrogen_storage description: The inclusion retains cyanophycin as a temporary nitrogen reserve. evidence: - reference: DOI:10.1128/AEM.01298-18 snippet: cyanophycin can be used as a temporary nitrogen storage notes: Scientific abstract clause. PCC 6803 wild-type versus cphA-deletion comparisons support condition-dependent storage during fluctuating or limiting nitrogen supply and light/dark cycles, not a universal fitness advantage. Granule-loss confirmation is reported as data not shown; no complementation experiment is claimed. discussions: - discussion_id: cyanophycin-granule-identity prompt: Keep inclusion morphology distinct from polymer and sequence identity. kind: CURATION_TODO status: OPEN rationale: Uses intracellular inclusion traitmech:000066 like PHA and polyphosphate granules. CHEBI:65318 is a chemical grounding only; CphA activity and family membership are not equivalent traits. CGP names the polymer, not an exact granule synonym. No trait xrefs, exact synonyms or SSSOM equivalences are asserted. Do not require spherical shape, fixed size, constitutive occurrence, or an invariant amino-acid ratio. posed_by: codex posed_date: '2026-10-07' - discussion_id: cyanophycin-granule-mechanism-scope prompt: Resolve strain-specific assembly and degradation mechanisms separately. kind: KNOWLEDGE_GAP status: OPEN rationale: The 2001 enzyme paper calls cyanophycin unique to cyanobacteria, but the 2018 primary paper also documents its distribution in heterotrophic bacteria; no cyanobacteria-only restriction is imposed. Soluble engineered polymers do not alone establish granules. The graph integrates distinct source taxa rather than transferring PCC 6308 CphA evidence to the ATCC 51142 example. PCC 6803 without a substrain designation does not establish the Kazusa-specific UniProt instance. Surface localization and magnesium effects in cell extracts do not prove a universal in-vivo assembly requirement. posed_by: codex posed_date: '2026-10-07' curation_history: - timestamp: '2026-10-08T04:30:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added cyanophycin granule with four primary references, bounded verbatim excerpts, a natural ATCC 51142 example and a five-node mechanistic graph. Verified PCC 6308 CphA protein/family and polymer identity separately from morphology. Ignored-and-hidden novelty and current-main/worktree/complete-open-PR reservation checks support 000673 and v549 block 1062600-1062699. Existing records unchanged. llm_assisted: true - timestamp: '2026-10-08T04:29:03Z' curator: codex action: CORRECT_CURATION_PROVENANCE changes: 'Corrected provenance for #1816 without rewriting the initial event: its 04:30:00Z timestamp was mistakenly set ahead of execution. The initial record was already written before the repository CREATE history timestamp 2026-10-08T04:28:08Z, an observed upper bound, not an exact reconstructed write time. This correction uses the directly observed UTC clock; biological content is unchanged.' llm_assisted: true