identifier: traitmech:000264 label: Sirona system definition: A phage defense system in which an organism possesses a Sirona locus represented by a VCA0356 profile that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1126/science.ads0768 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Sirona synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: VCA0356 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1126/science.ads0768 snippet: nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions notes: Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems. - reference: DOI:10.1126/science.ads0768 snippet: Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest notes: Darracq et al. support a nonmechanistic system record that does not assert a resolved Sirona trigger, effector output, or pathway. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Sirona | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems notes: The DefenseFinder model registry maps the named Sirona system to the Darracq et al. SCI antiphage-system paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Sirona__VCA0356 | | Sirona notes: The DefenseFinder HMM inventory records VCA0356 in the Sirona model namespace. causal_graphs: - graph_id: sirona_locus_restricts_phage title: Sirona loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Sirona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Sirona as a named SCI-derived anti-phage system with a VCA0356 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: sirona_locus label: Sirona locus node_type: GENETIC_ELEMENT description: A Sirona anti-phage defense locus represented in DefenseFinder by a VCA0356 profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Sirona system. - node_id: sirona_system_trait label: Sirona system node_type: TRAIT grounding: traitmech:000264 description: Possession of a genome-encoded Sirona 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: sirona_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Sirona to an SCI anti-phage-system discovery paper and represents Sirona loci through the VCA0356 component profile. evidence: - reference: DOI:10.1126/science.ads0768 snippet: nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions notes: Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Sirona registry row maps to the Sirona system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Sirona__VCA0356 | | Sirona notes: The DefenseFinder HMM inventory supports VCA0356 as the Sirona component profile. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: sirona_system_trait description: Sirona-mediated phage restriction realizes the Sirona system trait. evidence: - reference: DOI:10.1126/science.ads0768 snippet: Most of these novel systems have little or no similarity to previously known ones notes: Darracq et al. place the Sirona discovery cohort in a set of novel bacterial systems that protect against phages. - subject: sirona_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Sirona system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1126/science.ads0768 snippet: We also demonstrate that nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions notes: Darracq et al. support treating the Sirona source cohort as novel bacterial anti-phage systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Sirona | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems notes: DefenseFinder associates Sirona with the Darracq et al. bacterial antiphage-system paper. discussions: - discussion_id: sirona-mechanism-gap prompt: Resolve Sirona phage triggers and effector outputs before minting narrower Sirona mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Darracq et al. and DefenseFinder support Sirona as a named anti-phage system with a VCA0356 profile, 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#sirona_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T04:27:15Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Sirona system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v141. llm_assisted: true - timestamp: '2026-09-19T04:32:33Z' curator: codex action: EDIT changes: Reduced repeated DefenseFinder registry snippets in the Sirona causal graph after the evidence snippet audit flagged the same registry row on three edges. llm_assisted: true