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cyanophycin granule

traitmech:000673 · CLASS · PROPOSED

An intracellular storage inclusion composed of cyanophycin, a nonribosomal arginine- and aspartate-rich polymer serving as a nitrogen reserve.

Trait evidence (1)

  • DOI:10.1007/s002030100281
    Cyanophycin granules reached a maximum after the peak of nitrogenase activity and eventually were utilized completely.

    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.

CphA supplies polymer for cyanophycin storage granules

A source-bounded synthesis, material-localization and nitrogen-storage sketch, not a claim that every inclusion shares one regulation.

MECHANISTIC · 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.

Loading graph…

CphA supplies polymer for cyanophycin storage granules Interactive directed graph showing evidence-backed causal relationships for cyanophycin granule.

Edge evidence

  • cyanophycin synthetase CphA enables cyanophycin synthesis RO:0002327

    Purified PCC 6308 CphA catalyzes polymer synthesis.

    • DOI:10.1128/AEM.67.5.2176-2182.2001 which catalyzed the incorporation of arginine and aspartic acid into cyanophycin 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.
  • cyanophycin synthesis has output cyanophycin macromolecule RO:0002234

    The assayed reaction incorporates amino acids into cyanophycin.

    • DOI:10.1128/AEM.67.5.2176-2182.2001 which catalyzed the incorporation of arginine and aspartic acid into cyanophycin 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.
  • cyanophycin macromolecule located in cyanophycin granule biolink:located_in

    Accumulated cyanophycin forms the material of the inclusion.

    • DOI:10.1128/AEM.01298-18 Cyanophycin accumulates in the form of opaque and light-scattering granules in the cell 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.
  • cyanophycin granule contributes to temporary nitrogen storage RO:0002326

    The inclusion retains cyanophycin as a temporary nitrogen reserve.

    • DOI:10.1128/AEM.01298-18 cyanophycin can be used as a temporary nitrogen storage 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.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
cyanophycin synthetase CphA UniProtKB:P56947
Cyanophycin synthetase (cphA) 		Geminocystis herdmanii PCC 6308
NCBITaxon:113355 		REVIEWED
retrieved 2026-10-08 · entry v91 · sequence v2

PCC 6308 enzyme catalyzes cyanophycin synthesis; functional expression and purification used recombinant E. coli, not a natural E. coli phenotype.

  • DOI:10.1007/s002030000206 The functionality of cphA was proven by heterologous expression of active enzyme and synthesis of cyanophycin in Escherichia coli 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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/AEM.01298-18

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Crocosphaera subtropica ATCC 51142 NCBITaxon:43989 DOI:10.1007/s002030100281 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.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Keep inclusion morphology distinct from polymer and sequence identity.

CURATION TODO OPEN cyanophycin-granule-identity · raised by codex · 2026-10-07

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolve strain-specific assembly and degradation mechanisms separately.

KNOWLEDGE GAP OPEN cyanophycin-granule-mechanism-scope · raised by codex · 2026-10-07

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · CORRECT_CURATION_PROVENANCE · codex

    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.

Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed cyanophycin storage granule

      Minted traitmech:000673 under intracellular inclusion without modifying existing records. Four primary DOI sources support a natural ATCC 51142 example and a five-node, four-edge source-bounded graph. Protein evidence anchors reviewed UniProtKB:P56947 to Geminocystis herdmanii PCC 6308, distinct from the expression host and canonical trait taxon; InterPro:IPR011810 and CHEBI:65318 were authority checked. Full publisher text was read for 2018 cell biology and 2001 purified enzyme work; the 2000 expression and Li 2001 accumulation sources were directly read as scientific abstracts. Actual figure images were not inspected. Reserved v549 METPO:1062600 within block 1062600-1062699 after ignored-and-hidden main, worktree, and complete open-PR reservation checks. Parent context from v5 retains identity and hierarchy with only its cohort subset updated. Guarded writer is dry-run by default and validates before writing.

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  • · codex
    • EDIT — Append correction for initial event timestamp (#1816)

      The initial MINTED_TRAITMECH_ID timestamp 2026-10-08T04:30:00Z was estimated ahead of actual execution. The record had already been written before history/records/cyanophycin_granule/2026-10-08T042808Z-codex-f1df51.yaml was scaffolded at 04:28:08Z. Retained that original per-record event and repository CREATE history unchanged; appended CORRECT_CURATION_PROVENANCE with an observed UTC clock timestamp and an explicit write-time upper bound, not an invented exact time. Biological content is unchanged. Writer replay includes the correction and accepts only the exact original preimage or corrected record. The add-trait skill now requires current-clock timestamps and append-only corrections.

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