identifier: traitmech:000367 label: RnlAB system definition: A phage defense system in which an organism possesses a genome-encoded RnlAB toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring RnlAB__RnlA and RnlAB__RnlB. definition_source: DOI:10.1534/genetics.110.121798 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: RnlAB synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: RnlAB__RnlA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: RnlAB__RnlB synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: PMID:20980243 snippet: RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. notes: Koga et al. frame RnlA-dependent RNase LS activity as a potential antagonist of bacteriophage T4 dmd mutants. - reference: PMID:20980243 snippet: Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. notes: Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the neighboring cognate antitoxin gene. - reference: PMID:20980243 snippet: Pull-down analysis showed a specific interaction between RnlA and RnlB. notes: Koga et al. support direct RnlA/RnlB interaction by pull-down analysis. - reference: PMID:20980243 snippet: All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system. notes: Koga et al. define rnlA-rnlB as a new toxin-antitoxin system. - reference: PMID:22403819 snippet: Predicted proteins encoded by these two ORFs were found to share a weak homology with RnlA and RnlB, respectively, a toxin–antitoxin system encoded on the E. coli K-12 chromosome. notes: Otsuka and Yonesaki describe RnlA/RnlB as a toxin-antitoxin system encoded on the Escherichia coli K-12 chromosome. - reference: PMID:22403819 snippet: T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins. notes: Otsuka and Yonesaki support T4 Dmd as a phage antitoxin that suppresses RnlA toxicity by direct interaction. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system notes: The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t" notes: The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RnlAB__RnlA | RnlAB__RnlA | RnlAB | Custom | 20 |' notes: The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RnlAB__RnlB | RnlAB__RnlB | RnlAB | Custom | 20 |' notes: The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB. canonical_examples: - taxon_id: NCBITaxon:83333 taxon_label: Escherichia coli K-12 note: Otsuka and Yonesaki describe the RnlA/RnlB toxin-antitoxin system as encoded on the Escherichia coli K-12 chromosome. reference: DOI:10.1111/j.1365-2958.2012.07975.x causal_graphs: - graph_id: rnlab_locus_antagonizes_t4_dmd_mutants title: RnlAB loci support RnlA-dependent RNase LS activity description: Conservative system-level sketch linking possession of an RnlAB locus to RnlA-dependent RNase LS activity against bacteriophage T4 dmd mutants without asserting a wild-type-phage trigger, broad phage host range, or exact RnlAB profile-to-activity mapping. scope_status: NONMECHANISTIC scope_notes: The graph captures RnlAB as a named DefenseFinder two-profile phage-defense system while leaving natural phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping unresolved. nodes: - node_id: rnlab_locus label: RnlAB locus node_type: GENETIC_ELEMENT description: A toxin-antitoxin locus represented by RnlAB__RnlA and RnlAB__RnlB profiles. - node_id: rnla_dependent_rnase_ls_activity label: RnlA-dependent RNase LS activity node_type: BIOLOGICAL_PROCESS description: RNase LS activity encoded by rnlA and controlled by rnlB, with RnlA capable of cleaving T4 mRNAs when phage Dmd is absent. - node_id: rnlab_system_trait label: RnlAB system node_type: TRAIT grounding: traitmech:000367 description: Possession of a genome-encoded RnlAB toxin-antitoxin 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: rnlab_locus predicate: contributes to predicate_id: RO:0002326 object: rnla_dependent_rnase_ls_activity description: Koga et al. show that rnlA encodes the RNase LS toxin and rnlB encodes the cognate antitoxin; DefenseFinder models RnlAB as a two-profile system. evidence: - reference: PMID:20980243 snippet: Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. notes: Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the antitoxin gene. - reference: PMID:20980243 snippet: Pull-down analysis showed a specific interaction between RnlA and RnlB. notes: Koga et al. show that RnlA and RnlB specifically interact. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system notes: The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t" notes: The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RnlAB__RnlA | RnlAB__RnlA | RnlAB | Custom | 20 |' notes: The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RnlAB__RnlB | RnlAB__RnlB | RnlAB | Custom | 20 |' notes: The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB. - subject: rnla_dependent_rnase_ls_activity predicate: confers predicate_id: METPO:2007700 object: rnlab_system_trait description: RnlA-dependent RNase LS activity against T4 dmd-mutant mRNAs realizes the RnlAB system trait. evidence: - reference: PMID:20980243 snippet: RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. notes: Koga et al. support RNase LS antagonism of T4 dmd-mutant reproduction. - reference: PMID:22403819 snippet: T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins. notes: Otsuka and Yonesaki show phage Dmd can suppress RnlA toxicity by direct interaction. - subject: rnlab_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: RnlAB system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system notes: The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RnlAB\tRnlAB\t2\t2\tRnlAB__RnlA, RnlAB__RnlB\t\t\t" notes: The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles. discussions: - discussion_id: rnlab-phage-breadth-evasion-gap prompt: Resolve natural RnlAB phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping before minting narrower RnlAB mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Koga et al. support RnlA/RnlB as an Escherichia coli K-12 toxin-antitoxin system whose RNase LS activity can antagonize T4 dmd mutants, Otsuka and Yonesaki show that T4 phage Dmd suppresses RnlA toxicity, and DefenseFinder models RnlAB as a two-profile system with RnlAB__RnlA and RnlAB__RnlB markers. Natural phage breadth, wild-type T4 evasion, non-T4 activation contexts, and profile-to-activity mapping remain unresolved. evidence: - reference: PMID:22403819 snippet: T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins. notes: Otsuka and Yonesaki show that T4 Dmd suppresses RnlA toxicity, marking phage evasion as a real boundary around RnlAB mechanism curation. attaches_to: - causal_graphs#rnlab_locus_antagonizes_t4_dmd_mutants posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T13:54:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted RnlAB 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_v244. llm_assisted: true