identifier: traitmech:000480 label: TIR-I system definition: A phage defense system in which an organism possesses a TIR-I locus, represented in the pinned DefenseFinder HMM inventory by TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles, that can inhibit bacteriophage plaquing. definition_source: DOI:10.1038/s41467-024-51738-3 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: TIR-I synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-024-51738-3 - synonym_text: TIR-I__TIR-I_A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: TIR-I__TIR-I_B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1038/s41467-024-51738-3 snippet: Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX notes: Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets. - reference: DOI:10.1038/s41467-024-51738-3 snippet: The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control notes: Wang et al. assayed cloned Escherichia coli TIR systems by efficiency-of-plating reduction against a phage panel. - reference: DOI:10.1038/s41467-024-51738-3 snippet: TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form notes: Wang et al. found that TIR-I, TIR-III, and TIR-IV systems occur in diverse domain contexts, while TIR-VII and TIR-VIII systems were recovered in a single form. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TIR-I | 10\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |' notes: The pinned DefenseFinder article registry maps the named TIR-I system to the Wang et al. TIR-domain anti-phage system paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TIR-I__TIR-I_A | | TIR-I | Custom | 300 | | TIR-I__TIR-I_B | | TIR-I | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace. causal_graphs: - graph_id: tir_i_locus_inhibits_phage_plaquing title: TIR-I loci inhibit bacteriophage plaquing description: Conservative system-level sketch linking a TIR-I locus to inhibited bacteriophage plaquing and TIR-I system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures TIR-I at TIR-system and anti-phage assay level without asserting exact native-host breadth, one universal domain architecture, a direct phage trigger, TIR-domain catalytic output, accession-level components, or a DefenseFinder detection rule absent from the pinned rules table. nodes: - node_id: tir_i_locus label: TIR-I locus node_type: GENETIC_ELEMENT description: A TIR-I phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles. - node_id: inhibited_phage_plaquing label: inhibited bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing by bacteriophages in cells carrying a complete TIR-I system. - node_id: tir_i_system_trait label: TIR-I system node_type: TRAIT grounding: traitmech:000480 description: Possession of a genome-encoded TIR-I 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: tir_i_locus predicate: contributes to predicate_id: RO:0002326 object: inhibited_phage_plaquing description: Wang et al. linked TIR-I to anti-phage activity, and DefenseFinder records two custom TIR-I system profiles. evidence: - reference: DOI:10.1038/s41467-024-51738-3 snippet: Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX notes: Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TIR-I__TIR-I_A | | TIR-I | Custom | 300 | | TIR-I__TIR-I_B | | TIR-I | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace. - subject: inhibited_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: tir_i_system_trait description: TIR-I-mediated inhibition of bacteriophage plaquing realizes the TIR-I system trait. evidence: - reference: DOI:10.1038/s41467-024-51738-3 snippet: The defense activity of the TIR systems against each phage was determined based on their ability to inhibit plaque formation compared to the pSEC1 empty vector control notes: Wang et al. measured cloned TIR-system activity by inhibited plaque formation relative to an empty-vector control. - subject: tir_i_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: TIR-I system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TIR-I | 10\.1038/s41467-024-51738-3 | The role of TIR domain-containing proteins in bacterial defense against phages |' notes: The pinned DefenseFinder article registry maps the named TIR-I system to the Wang et al. TIR-domain anti-phage system paper. discussions: - discussion_id: tir-i-detection-trigger-gap prompt: Resolve TIR-I native host breadth, the TIR-I__TIR-I_A and TIR-I__TIR-I_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-I mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Wang et al. support TIR-I as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-I occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-I row. This first record therefore does not assert profile requirement logic, accession-level components, a universal domain architecture, or a direct phage trigger. evidence: - reference: DOI:10.1038/s41467-024-51738-3 snippet: Twelve systems have defense activities against a variable number of phages, and 9 of them are new defense systems and named TIR-I to IX notes: Wang et al. report that TIR-I belongs to nine newly named TIR-domain anti-phage defense systems with activity against variable phage subsets. - reference: DOI:10.1038/s41467-024-51738-3 snippet: TIR-I, TIR-III, and TIR-IV systems appear in diverse domains contexts, whereas the TIR-VII and TIR-VIII systems were found in a single form notes: Wang et al. support unresolved TIR-I domain architecture breadth. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TIR-I__TIR-I_A | | TIR-I | Custom | 300 | | TIR-I__TIR-I_B | | TIR-I | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records TIR-I__TIR-I_A and TIR-I__TIR-I_B custom profiles under the TIR-I system namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list TIR-I, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#tir_i_locus_inhibits_phage_plaquing posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T02:41:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted TIR-I 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 TIR-system and phage-plaquing level because TIR-I direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v357. llm_assisted: true - timestamp: '2026-09-30T02:41:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed TIR-I system during canonical-example issue 444 enforcement and left canonical_examples empty because Wang et al. support heterologous E. coli MG1655 plaque assays and DefenseFinder TIR-I HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-I activity. No paid research was used. llm_assisted: true