identifier: traitmech:000376 label: Rst gop-beta-cII system definition: A phage defense system in which an organism possesses a P4-like gop-beta-cII locus represented by DefenseFinder as the Rst_gop_beta_cll model and experimentally linked to lambda and P1 phage restriction. definition_source: DOI:10.1016/j.chom.2022.02.018 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: gop-β-cII synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2022.02.018 - synonym_text: Rst_gop_beta_cll synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, β, and cII, with gop and β likely acting as a toxin-antitoxin pair notes: Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: We report that gop-β-cII forms an anti-phage system that protects against λ and P1. notes: Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage notes: Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Rst_gop_beta_cll | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems notes: The DefenseFinder article registry maps the named Rst_gop_beta_cll system to the Rousset et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta, Rst_gop_beta_cll__cll,\ \ Rst_gop_beta_cll__gop\t\t\t" notes: The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_gop_beta_cll__beta | Rst_gop_beta_cll__beta | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__cll | Rst_gop_beta_cll__cll | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__gop | Rst_gop_beta_cll__gop | Rst_gop_beta_cll | Custom | 20 |' notes: The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace. causal_graphs: - graph_id: rst_gop_beta_cll_locus_restricts_lambda_p1 title: Rst gop-beta-cII loci restrict lambda and P1 phages description: Conservative system-level sketch linking a P4 gop-beta-cII locus to lambda and P1 phage restriction. scope_status: NONMECHANISTIC scope_notes: The graph captures gop-beta-cII as a named DefenseFinder three-profile phage-defense system while leaving natural host breadth, the direct phage trigger, the gop and beta toxin-antitoxin interpretation, cII activity, and profile-to-gene mapping unresolved. nodes: - node_id: rst_gop_beta_cll_locus label: Rst gop-beta-cII locus node_type: GENETIC_ELEMENT description: A P4-like gop-beta-cII phage-defense locus represented by beta, cll, and gop DefenseFinder profiles. - node_id: lambda_and_p1_phage_restriction label: lambda and P1 phage restriction node_type: BIOLOGICAL_PROCESS description: Restriction of bacteriophages lambda and P1 by the gop-beta-cII locus. - node_id: rst_gop_beta_cll_system_trait label: Rst gop-beta-cII system node_type: TRAIT grounding: traitmech:000376 description: Possession of a genome-encoded gop-beta-cII 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: rst_gop_beta_cll_locus predicate: contributes to predicate_id: RO:0002326 object: lambda_and_p1_phage_restriction description: Rousset et al. linked gop-beta-cII to lambda and P1 phage protection, and DefenseFinder models Rst_gop_beta_cll as a three-profile system. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, β, and cII, with gop and β likely acting as a toxin-antitoxin pair notes: Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage notes: Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta,\ \ Rst_gop_beta_cll__cll, Rst_gop_beta_cll__gop\t\t\t" notes: The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_gop_beta_cll__beta | Rst_gop_beta_cll__beta | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__cll | Rst_gop_beta_cll__cll | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__gop | Rst_gop_beta_cll__gop | Rst_gop_beta_cll | Custom | 20 |' notes: The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace. - subject: lambda_and_p1_phage_restriction predicate: confers predicate_id: METPO:2007700 object: rst_gop_beta_cll_system_trait description: Restriction of lambda and P1 phages realizes the Rst gop-beta-cII system trait. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: We report that gop-β-cII forms an anti-phage system that protects against λ and P1. notes: Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: When compared with a control vector encoding a green fluorescent protein (GFP), seven systems provided robust and reproducible resistance to at least one phage notes: Rousset et al. cloned P4/P2 hotspot systems under native promoters and measured reproducible phage resistance against their coliphage panel. - subject: rst_gop_beta_cll_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Rst gop-beta-cII system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems notes: Rousset et al. frame the P4-like satellite hotspot that contains gop-beta-cII as a reservoir of anti-phage systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Rst_gop_beta_cll | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems notes: The DefenseFinder article registry maps the named Rst_gop_beta_cll system to the Rousset et al. preprint. discussions: - discussion_id: rst-gop-beta-cll-mechanism-gap prompt: Resolve Rst_gop_beta_cll natural host breadth, exact beta and cll gene correspondence, direct phage trigger, and Gop or beta toxin-antitoxin activities before minting narrower P4 gop-beta-cII mechanism traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Rousset et al. support a canonical P4 gop-beta-cII system that protects against lambda and P1, and DefenseFinder represents Rst_gop_beta_cll as a required beta/cll/gop three-profile model. This first system-level record leaves natural host breadth, profile-to-gene mapping, the direct phage trigger, and the gop, beta, or cII effector logic unresolved. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: The well-characterized P4 satellite (NC_001609) carries at this position the non-essential genes gop, β, and cII, with gop and β likely acting as a toxin-antitoxin pair notes: Rousset et al. describe the canonical P4 satellite gop, beta, and cII locus before testing it for anti-phage activity. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: We report that gop-β-cII forms an anti-phage system that protects against λ and P1. notes: Rousset et al. directly identify gop-beta-cII as an anti-phage system that protects against lambda and P1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_gop_beta_cll\tRst_gop_beta_cll\t3\t3\tRst_gop_beta_cll__beta, Rst_gop_beta_cll__cll,\ \ Rst_gop_beta_cll__gop\t\t\t" notes: The DefenseFinder rules table models Rst_gop_beta_cll as a three-profile system requiring beta, cll, and gop profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_gop_beta_cll__beta | Rst_gop_beta_cll__beta | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__cll | Rst_gop_beta_cll__cll | Rst_gop_beta_cll | Custom | 20 | | Rst_gop_beta_cll__gop | Rst_gop_beta_cll__gop | Rst_gop_beta_cll | Custom | 20 |' notes: The DefenseFinder HMM inventory records custom beta, cll, and gop profiles under the Rst_gop_beta_cll system namespace. attaches_to: - causal_graphs#rst_gop_beta_cll_locus_restricts_lambda_p1 posed_by: codex posed_date: '2026-09-26' curation_history: - timestamp: '2026-09-26T08:43:24Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Rst gop-beta-cII 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_v253. llm_assisted: true - timestamp: '2026-09-26T08:53:24Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Rst gop-beta-cII system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4 gop-beta-cII locus tested in Escherichia coli and a DefenseFinder system model, but not a direct native microbial isolate exemplar with experimentally verified Rst_gop_beta_cll activity. No paid research was used. llm_assisted: true