identifier: traitmech:000482 label: TIR-IV system definition: A phage defense system in which an organism possesses a TIR-IV locus, represented in the pinned DefenseFinder HMM inventory by TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_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-IV synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-024-51738-3 - synonym_text: TIR-IV__TIR-IV_A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: TIR-IV__TIR-IV_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-IV 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-IV, like TIR-I and TIR-III, occurs in diverse domain contexts. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| TIR-IV | 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-IV 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-IV__TIR-IV_A | | TIR-IV | Custom | 100 | | TIR-IV__TIR-IV_B | | TIR-IV | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV system namespace. causal_graphs: - graph_id: tir_iv_locus_inhibits_phage_plaquing title: TIR-IV loci inhibit bacteriophage plaquing description: Conservative system-level sketch linking a TIR-IV locus to inhibited bacteriophage plaquing and TIR-IV system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures TIR-IV 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_iv_locus label: TIR-IV locus node_type: GENETIC_ELEMENT description: A TIR-IV phage-defense locus represented in the pinned DefenseFinder HMM inventory by TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_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-IV system. - node_id: tir_iv_system_trait label: TIR-IV system node_type: TRAIT grounding: traitmech:000482 description: Possession of a genome-encoded TIR-IV 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_iv_locus predicate: contributes to predicate_id: RO:0002326 object: inhibited_phage_plaquing description: Wang et al. linked TIR-IV to anti-phage activity, and DefenseFinder records two custom TIR-IV 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-IV 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-IV__TIR-IV_A | | TIR-IV | Custom | 100 | | TIR-IV__TIR-IV_B | | TIR-IV | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV system namespace. - subject: inhibited_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: tir_iv_system_trait description: TIR-IV-mediated inhibition of bacteriophage plaquing realizes the TIR-IV 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_iv_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: TIR-IV 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-IV | 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-IV system to the Wang et al. TIR-domain anti-phage system paper. discussions: - discussion_id: tir-iv-detection-trigger-gap prompt: Resolve TIR-IV native host breadth, the TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B profile-to-component mapping, phage-trigger specificity, TIR-domain output chemistry, and rule-level DefenseFinder detection criteria before minting narrower TIR-IV mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Wang et al. support TIR-IV as one of nine newly named TIR-domain anti-phage defense systems and note that TIR-IV occurs in diverse domain contexts. The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profile rows, but the pinned DefenseFinder rules table has no TIR-IV 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-IV 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-IV domain architecture breadth. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| TIR-IV__TIR-IV_A | | TIR-IV | Custom | 100 | | TIR-IV__TIR-IV_B | | TIR-IV | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records TIR-IV__TIR-IV_A and TIR-IV__TIR-IV_B custom profiles under the TIR-IV 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-IV, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#tir_iv_locus_inhibits_phage_plaquing posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T04:28:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted TIR-IV system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at TIR-system and phage-plaquing level because TIR-IV direct triggers, profile-to-component mapping, and rule-level DefenseFinder criteria remain unresolved; the replacement placeholder is reserved in proposals/metpo_traitmech_v359. llm_assisted: true - timestamp: '2026-09-30T04:28:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed TIR-IV 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-IV HMM rows, but the first-pass curation did not recover a direct named native microbial isolate exemplar with experimentally verified endogenous TIR-IV activity. No paid research was used. llm_assisted: true