identifier: traitmech:000352 label: Gao-RL system definition: A phage defense system in which an organism possesses a Gao_RL locus represented by DefenseFinder as a four-profile model requiring Gao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, and Gao_RL__RL_D. definition_source: DOI:10.1126/science.aba0372 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Gao_RL synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Gao_RL__RL_A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Gao_RL__RL_B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Gao_RL__RL_C synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Gao_RL__RL_D 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_RL | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_RL 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_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D" notes: The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_A | Gao_RL__RL_A | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_A under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_B | Gao_RL__RL_B | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_B under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_C | Gao_RL__RL_C | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_C under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_D | Gao_RL__RL_D | Gao_RL | Custom | 100 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_D under Gao_RL. causal_graphs: - graph_id: gao_rl_locus_restricts_phage title: Gao-RL loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Gao_RL locus to Gao et al. antiviral cassette defense without asserting the unresolved RL component activities. scope_status: NONMECHANISTIC scope_notes: The graph captures Gao-RL as a named DefenseFinder four-profile Gao-family system while leaving natural hosts, RL_A/RL_B/RL_C/RL_D protein functions, phage triggers, and direct effector activity unresolved. nodes: - node_id: gao_rl_locus label: Gao_RL locus node_type: GENETIC_ELEMENT description: A DefenseFinder Gao_RL phage-defense locus represented by custom RL_A through RL_D profiles. - 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_rl_system_trait label: Gao-RL system node_type: TRAIT grounding: traitmech:000352 description: Possession of a genome-encoded Gao-RL 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_rl_locus predicate: contributes to predicate_id: RO:0002326 object: gao_2020_antiviral_cassette_defense description: DefenseFinder maps Gao_RL to the Gao et al. systematic antiphage-system discovery paper and models it as a four-profile system requiring RL_A through RL_D. 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_RL | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_RL 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_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D" notes: The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_A | Gao_RL__RL_A | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_A under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_B | Gao_RL__RL_B | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_B under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_C | Gao_RL__RL_C | Gao_RL | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_C under Gao_RL. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_RL__RL_D | Gao_RL__RL_D | Gao_RL | Custom | 100 |' notes: The DefenseFinder HMM inventory records Gao_RL__RL_D under Gao_RL. - subject: gao_2020_antiviral_cassette_defense predicate: confers predicate_id: METPO:2007700 object: gao_rl_system_trait description: Gao_RL-associated antiviral cassette defense realizes the Gao-RL 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_rl_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Gao-RL 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_RL | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_RL 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_RL\tGao_RL\t4\t4\tGao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, Gao_RL__RL_D" notes: The DefenseFinder rules table models Gao_RL as a four-profile system requiring RL_A through RL_D profiles. discussions: - discussion_id: gao-rl-mechanism-gap prompt: Resolve Gao_RL natural hosts, RL_A/RL_B/RL_C/RL_D component functions, phage triggers, and effector activity before minting narrower Gao_RL 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_RL as a four-profile system. The exact natural host breadth, RL component identities, phage trigger, and profile-to-activity mapping remain unresolved. attaches_to: - causal_graphs#gao_rl_locus_restricts_phage posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T01:39:05Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Gao-RL 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_v229. llm_assisted: true