identifier: traitmech:000422 label: CoCoNuT system definition: 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. definition_source: DOI:10.7554/eLife.94800.3 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: CoCoNuT synonym_type: EXACT_SYNONYM source: DOI:10.7554/eLife.94800.3 - synonym_text: CoCoNut synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: CoCoNut-I-A__I-A_CnuB synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: CoCoNut-II__II_CnuH synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: CoCoNut-III-B__III-B_CnuHE synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.7554/eLife.94800.3 snippet: 'We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases' notes: Bell et al. name CoCoNuTs as coiled-coil nuclease tandem systems in an uncharacterized McrBC Type IV restriction branch. - reference: DOI:10.7554/eLife.94800.3 snippet: We classified the CoCoNuTs into three types and seven subtypes based on the GTPase domain phylogeny and conserved genomic context notes: Bell et al. classify CoCoNuTs into multiple types and subtypes using GTPase phylogeny and conserved genomic context. - reference: DOI:10.7554/eLife.94800.3 snippet: all suggesting that the CoCoNuTs target RNA notes: Bell et al. interpret CoCoNuT domain architecture as predictive of RNA targeting. - reference: DOI:10.7554/eLife.94800.3 snippet: Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs notes: Bell et al. predict that many CoCoNuTs might also target DNA via McrC nuclease homologs. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| CoCoNut | 10\.7554/eLife\.94800\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ' notes: The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-I-A__I-A_CnuB | | CoCoNut-I-A | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-I-A__I-A_CnuB as a custom CoCoNut profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-II__II_CnuH | | CoCoNut-II | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-II__II_CnuH as a custom CoCoNut profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-III-B__III-B_CnuHE | | CoCoNut-III-B | Custom | 750 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-III-B__III-B_CnuHE as a custom CoCoNut profile. causal_graphs: - graph_id: coconut_system_family_hierarchy title: CoCoNuT loci are predicted Type IV restriction systems description: Conservative system-level sketch linking CoCoNuT system possession to phage defense without resolving individual components or a direct molecular output. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: coconut_system_trait label: CoCoNuT system node_type: TRAIT grounding: traitmech:000422 description: Possession of a genome-encoded CoCoNuT Type IV restriction-system family locus. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: coconut_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: CoCoNuT system possession is treated as a phage-defense-system trait. evidence: - reference: DOI:10.7554/eLife.94800.3 snippet: largely uncharacterized prokaryotic antiphage restriction systems notes: Bell et al. frame EVE/McrB-like Type IV restriction-system diversity in the context of prokaryotic antiphage restriction. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| CoCoNut | 10\.7554/eLife\.94800\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ' notes: The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article. discussions: - discussion_id: coconut-defensefinder-model-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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: - reference: DOI:10.7554/eLife.94800.3 snippet: We classified the CoCoNuTs into three types and seven subtypes based on the GTPase domain phylogeny and conserved genomic context notes: Bell et al. classify CoCoNuTs into type and subtype groups using phylogeny and genomic context. - reference: DOI:10.7554/eLife.94800.3 snippet: all suggesting that the CoCoNuTs target RNA notes: Bell et al. predict RNA targeting from CoCoNuT component-domain architectures. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| CoCoNut | 10\.7554/eLife\.94800\.3 | CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA | ' notes: The pinned DefenseFinder article registry maps the CoCoNut source key to the Bell et al. versioned eLife article. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-I-A__I-A_CnuB | | CoCoNut-I-A | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-I-A__I-A_CnuB as a custom CoCoNut profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-II__II_CnuH | | CoCoNut-II | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-II__II_CnuH as a custom CoCoNut profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CoCoNut-III-B__III-B_CnuHE | | CoCoNut-III-B | Custom | 750 |' notes: The pinned DefenseFinder HMM inventory records CoCoNut-III-B__III-B_CnuHE as a custom CoCoNut profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list CoCoNut, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#coconut_system_family_hierarchy posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T01:05:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-09-28T01:05:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 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. llm_assisted: true