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CoCoNuT system

traitmech:000422 · CLASS · PROPOSED

A phage defense system in which an organism possesses a CoCoNuT locus from a coiled-coil nuclease tandem branch of McrBC Type IV restriction systems whose domain and genomic-context architecture predict RNA targeting and, in many CoCoNuTs, DNA targeting via McrC nuclease homologs.

Trait evidence (8)

CoCoNuT loci are predicted Type IV restriction systems

Conservative system-level sketch linking CoCoNuT system possession to phage defense without resolving individual components or a direct molecular output.

NONMECHANISTIC · The graph captures CoCoNuT at the named McrBC/Type IV system-family level with representative CoCoNut-I, CoCoNut-II, and CoCoNut-III DefenseFinder HMM rows. It does not assert exact profile-to-protein boundaries, direct RNA or DNA substrates, native host range, phage range, subtype boundaries, pseudo-CoCoNuT scope, CARF-regulated superoperon scope, or rule-level detection criteria.

CoCoNuT loci are predicted Type IV restriction systems Interactive directed graph showing evidence-backed causal relationships for CoCoNuT system.

Edge evidence

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.7554/eLife.94800.3

Parent traits (1)

Synonyms (5)

  • CoCoNuT EXACT_SYNONYM · DOI:10.7554/eLife.94800.3
  • CoCoNut RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  • CoCoNut-I-A__I-A_CnuB RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • CoCoNut-II__II_CnuH RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • CoCoNut-III-B__III-B_CnuHE RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

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

Discussions and Knowledge Gaps (1)

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

Resolve exact CoCoNuT type and subtype boundaries, native host breadth, direct RNA and DNA substrates, phage range, pseudo-CoCoNuT scope, CARF-regulated superoperon scope, and rule-level detection criteria before minting narrower CoCoNuT mechanism children.

KNOWLEDGE GAP OPEN coconut-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#coconut_system_family_hierarchy

Bell et al. support CoCoNuTs as a computationally defined McrBC/Type IV restriction branch predicted to target RNA and, for many loci, DNA; the pinned DefenseFinder HMM inventory records custom CoCoNut-I, CoCoNut-II, and CoCoNut-III profile rows. The pinned rules table has no CoCoNut row, and the first-pass record leaves exact profile-to-protein boundaries, pseudo-CoCoNuT inclusion, natural host breadth, phage range, and substrate-level mechanism unresolved.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted CoCoNuT system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at McrBC/Type IV system-family level because the pinned DefenseFinder CoCoNut HMM rows are not backed by a rules row; proposals/metpo_traitmech_v299 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed CoCoNuT system canonical_examples and left them empty because Bell et al. support computationally predicted CoCoNuT systems and DefenseFinder records CoCoNut HMM profiles, but the sources do not provide a direct native microbial isolate exemplar with experimentally verified endogenous CoCoNuT activity. No paid research was used.