identifier: traitmech:000309 label: Hypnos system definition: A phage defense system in which an organism possesses a Hypnos locus that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1016/j.chom.2024.07.007 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Hypnos synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: HyoA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1016/j.chom.2024.07.007 snippet: We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. notes: van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses. - reference: DOI:10.1016/j.chom.2024.07.007 snippet: Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates. notes: van den Berg et al. motivate a conservative system-level record that does not assert a resolved Hypnos trigger, effector output, or universal pathway. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Hypnos | 10\.1016/j\.chom\.2024\.07\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses notes: The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Hypnos__HyoA | | Hypnos notes: The DefenseFinder HMM inventory records Hypnos__HyoA in the Hypnos model namespace. causal_graphs: - graph_id: hypnos_locus_restricts_phage title: Hypnos loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Hypnos locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Hypnos as a named anti-phage system with a Hypnos__HyoA DefenseFinder HMM profile entry while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: hypnos_locus label: Hypnos locus node_type: GENETIC_ELEMENT description: A Hypnos anti-phage defense locus cataloged in DefenseFinder with a Hypnos__HyoA HMM profile entry. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Hypnos system. - node_id: hypnos_system_trait label: Hypnos system node_type: TRAIT grounding: traitmech:000309 description: Possession of a genome-encoded Hypnos phage-defense system. - 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: hypnos_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Hypnos to a eukaryotic-antiviral-homolog antiphage-system discovery paper and catalogs a Hypnos__HyoA HMM profile entry in the Hypnos model namespace. evidence: - reference: DOI:10.1016/j.chom.2024.07.007 snippet: We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. notes: van den Berg et al. validated six phage defense systems related to eukaryotic innate antiviral responses. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Hypnos | 10\.1016/j\.chom\.2024\.07\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses notes: The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Hypnos__HyoA | | Hypnos notes: The DefenseFinder HMM inventory records Hypnos__HyoA in the Hypnos model namespace. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: hypnos_system_trait description: Hypnos-mediated phage restriction realizes the Hypnos system trait. evidence: - reference: DOI:10.1016/j.chom.2024.07.007 snippet: We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. notes: van den Berg et al. validated six phage defense systems related to eukaryotic antiviral responses. - subject: hypnos_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Hypnos system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Hypnos | 10\.1016/j\.chom\.2024\.07\.007 | Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses notes: The DefenseFinder model registry maps the named Hypnos system to the van den Berg et al. antiphage-system discovery paper. discussions: - discussion_id: hypnos-mechanism-gap prompt: Resolve Hypnos phage triggers and effector outputs before minting narrower Hypnos mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: van den Berg et al. and DefenseFinder support Hypnos as a named anti-phage system with a Hypnos__HyoA HMM profile entry, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait. attaches_to: - causal_graphs#hypnos_locus_restricts_phage posed_by: codex posed_date: '2026-09-20' curation_history: - timestamp: '2026-09-20T13:10:22Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Hypnos 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; the replacement placeholder is reserved in proposals/metpo_traitmech_v186. llm_assisted: true