identifier: traitmech:000365 label: PfiAT system definition: A phage defense system in which an organism possesses a Pf4 prophage-encoded PfiAT toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring PfiAT__PfiA and PfiAT__PfiT. definition_source: DOI:10.1111/1751-7915.13570 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: PfiAT synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: PfiAT__PfiA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: PfiAT__PfiT synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: PMID:32246813 snippet: we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair. notes: Li et al. experimentally identify PA0729 and Rorf0727 in the Pf4 prophage as a PfiT/PfiA type II toxin-antitoxin pair. - reference: PMID:32246813 snippet: Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production. notes: Li et al. show that deleting pfiT increases Pf4 phage production. - reference: PMID:32246813 snippet: We thus suggest the toxin PA0729 be named PfiT for Pf4 inhibition toxin and Rorf0727 be named PfiA for PfiT antitoxin. notes: Li et al. name PA0729 as PfiT and Rorf0727 as PfiA. - reference: PMID:32246813 snippet: Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements. notes: Li et al. frame Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa notes: The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t" notes: The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PfiAT__PfiA | PfiAT__PfiA | PfiAT | Custom | 20 |' notes: The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PfiAT__PfiT | PfiAT__PfiT | PfiAT | Custom | 20 |' notes: The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT. causal_graphs: - graph_id: pfiat_locus_regulates_pf4_phage title: PfiAT loci regulate Pf4 prophage production description: Conservative system-level sketch linking possession of a PfiAT locus to PfiT/PfiA-dependent regulation of Pf4 phage production and immunity without asserting the cellular PfiT toxin target or natural host breadth. scope_status: NONMECHANISTIC scope_notes: The graph captures PfiAT as a named DefenseFinder two-profile Pf prophage system while leaving natural host breadth, the cellular target of PfiT in Pseudomonas, Pf4 phage-immunity coupling, and PfiAT profile-to-activity mapping unresolved. nodes: - node_id: pfiat_locus label: PfiAT locus node_type: GENETIC_ELEMENT description: A Pf prophage-encoded PfiAT toxin-antitoxin locus represented by PfiAT__PfiA and PfiAT__PfiT profiles. - node_id: pf4_phage_production_regulation label: Pf4 phage production regulation node_type: BIOLOGICAL_PROCESS description: Regulation of Pf4 phage production and Pf4 phage immunity by a prophage-encoded PfiT/PfiA toxin-antitoxin pair. - node_id: pfiat_system_trait label: PfiAT system node_type: TRAIT grounding: traitmech:000365 description: Possession of a genome-encoded PfiAT 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: pfiat_locus predicate: contributes to predicate_id: RO:0002326 object: pf4_phage_production_regulation description: Li et al. identify the Pf4 PA0729 and Rorf0727 locus as a PfiT/PfiA toxin-antitoxin pair whose pfiT toxin gene inhibits Pf4 production, and DefenseFinder models PfiAT as a two-profile system. evidence: - reference: PMID:32246813 snippet: we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair. notes: Li et al. experimentally identify PA0729 and Rorf0727 as a PfiT/PfiA toxin-antitoxin pair near the right attachment site of Pf4. - reference: PMID:32246813 snippet: Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production. notes: Li et al. show that pfiT inhibits Pf4 phage production. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa notes: The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t" notes: The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PfiAT__PfiA | PfiAT__PfiA | PfiAT | Custom | 20 |' notes: The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PfiAT__PfiT | PfiAT__PfiT | PfiAT | Custom | 20 |' notes: The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT. - subject: pf4_phage_production_regulation predicate: confers predicate_id: METPO:2007700 object: pfiat_system_trait description: PfiT/PfiA-dependent regulation of Pf4 phage production and immunity realizes the PfiAT system trait. evidence: - reference: PMID:32246813 snippet: Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements. notes: Li et al. support Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity. - subject: pfiat_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: PfiAT system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa notes: The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "PfiAT\tPfiAT\t2\t2\tPfiAT__PfiA, PfiAT__PfiT\t\t\t" notes: The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles. discussions: - discussion_id: pfiat-mechanism-gap prompt: Resolve natural PfiAT host breadth, the PfiT cellular target in Pseudomonas, Pf prophage production and immunity coupling, and PfiAT profile-to-activity mapping before minting narrower PfiAT mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Li et al. support PA0729/PfiT and Rorf0727/PfiA in the Pf4 prophage as a type II toxin-antitoxin pair that regulates Pf4 production and phage immunity, and DefenseFinder models PfiAT as a two-profile system with PfiAT__PfiA and PfiAT__PfiT markers. Natural host breadth, the cellular target of PfiT, Pf4 immunity coupling, and profile-to-activity mapping remain unresolved. evidence: - reference: PMID:32246813 snippet: Homologs of PfiT are also found in other Pseudomonas strains, and the cellular target of PfiT in Pseudomonas will be investigated in future studies. notes: Li et al. explicitly leave the PfiT cellular target unresolved. attaches_to: - causal_graphs#pfiat_locus_regulates_pf4_phage posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T12:25:36Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted PfiAT 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_v242. llm_assisted: true - timestamp: '2026-09-22T12:25:37Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 'Reviewed the PfiAT canonical_examples gap and left canonical_examples empty: the current evidence supports the Pf4 prophage PfiT/PfiA toxin-antitoxin pair, its control of Pf4 phage production and immunity, and the pinned DefenseFinder PfiAT profiles, but does not cite a directly observed natural microbial taxon with a source-backed PfiAT locus broad enough for a canonical example. No paid research was used.' llm_assisted: true