identifier: traitmech:000356 label: Gao-Ppl system definition: A phage defense system in which an organism possesses a Gao_Ppl locus represented by DefenseFinder as a single-profile model requiring Gao_Ppl__PplA. definition_source: DOI:10.1126/science.aba0372 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Gao_Ppl synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Gao_Ppl__PplA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Ppl | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA" notes: The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Ppl__PplA | Gao_Ppl__PplA | Gao_Ppl | Custom | 100 |' notes: The DefenseFinder HMM inventory records Gao_Ppl__PplA under Gao_Ppl. causal_graphs: - graph_id: gao_ppl_locus_restricts_phage title: Gao-Ppl loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Gao_Ppl locus to Gao et al. antiviral cassette defense without asserting the unresolved PplA component activity. scope_status: NONMECHANISTIC scope_notes: The graph captures Gao-Ppl as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, PplA protein function, phage triggers, and direct effector activity unresolved. nodes: - node_id: gao_ppl_locus label: Gao_Ppl locus node_type: GENETIC_ELEMENT description: A DefenseFinder Gao_Ppl phage-defense locus represented by a custom PplA profile. - node_id: gao_2020_antiviral_cassette_defense label: Gao 2020 antiviral cassette defense node_type: BIOLOGICAL_PROCESS description: Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign. - node_id: gao_ppl_system_trait label: Gao-Ppl system node_type: TRAIT grounding: traitmech:000356 description: Possession of a genome-encoded Gao-Ppl 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: gao_ppl_locus predicate: contributes to predicate_id: RO:0002326 object: gao_2020_antiviral_cassette_defense description: DefenseFinder maps Gao_Ppl to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring PplA. evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support bacteriophage protection by widespread antiviral gene cassettes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Ppl | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA" notes: The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Ppl__PplA | Gao_Ppl__PplA | Gao_Ppl | Custom | 100 |' notes: The DefenseFinder HMM inventory records Gao_Ppl__PplA under Gao_Ppl. - subject: gao_2020_antiviral_cassette_defense predicate: confers predicate_id: METPO:2007700 object: gao_ppl_system_trait description: Gao_Ppl-associated antiviral cassette defense realizes the Gao-Ppl system trait. evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support bacteriophage protection by widespread antiviral gene cassettes. - subject: gao_ppl_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Gao-Ppl system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Ppl | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Ppl system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Ppl\tGao_Ppl\t1\t1\tGao_Ppl__PplA" notes: The DefenseFinder rules table models Gao_Ppl as a single-mandatory-profile system with the Gao_Ppl__PplA profile. discussions: - discussion_id: gao-ppl-mechanism-gap prompt: Resolve Gao_Ppl natural hosts, PplA component function, phage triggers, and effector activity before minting narrower Gao_Ppl mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Ppl as a single-profile system. The exact natural host breadth, PplA component identity, phage trigger, and profile-to-activity mapping remain unresolved. attaches_to: - causal_graphs#gao_ppl_locus_restricts_phage posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T06:23:08Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Gao-Ppl 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_v233. llm_assisted: true