identifier: traitmech:000366 label: RloC system definition: A phage defense system in which an organism possesses a genome-encoded RloC locus represented by DefenseFinder as a one-profile model requiring RloC__RloC. definition_source: DOI:10.1111/j.1365-2958.2008.06387.x trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: RloC synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: RloC__RloC synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: PMID:18681940 snippet: The conserved bacterial protein RloC, a distant homologue of the tRNA(Lys) anticodon nuclease (ACNase) PrrC, is shown here to act as a wobble nucleotide-excising and Zn(++)-responsive tRNase. notes: Davidov and Kaufmann identify RloC as a conserved bacterial wobble nucleotide-excising, zinc-responsive tRNase related to PrrC. - reference: PMID:18681940 snippet: Geobacillus kaustophilus RloC expressed in Escherichia coli exhibited ACNase activity that differed from PrrC's in substrate preference and ability to excise the wobble nucleotide. notes: Davidov and Kaufmann support wobble nucleotide excision by Geobacillus kaustophilus RloC expressed in Escherichia coli. - reference: PMID:26031711 snippet: In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks. notes: Bitton et al. describe RloC ACNase regulation by an internal switch that responds to double-stranded DNA breaks. - reference: PMID:26031711 snippet: Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation. notes: Bitton et al. show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4, but not by a host-DNA-degradation mutant. - reference: PMID:26031711 snippet: Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction. notes: Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'RloC | 10\.1111/j\.1365-2958\.2008\.06387\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase' notes: The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t" notes: The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RloC__RloC | RloC__RloC | RloC | Custom | 120 |' notes: The DefenseFinder HMM inventory records RloC__RloC under RloC. causal_graphs: - graph_id: rloc_locus_triggers_dna_break_responsive_activation title: RloC loci encode DNA-break-responsive activation description: Conservative system-level sketch linking possession of a DefenseFinder RloC locus to DNA-break-responsive RloC anticodon nuclease activation without asserting natural host breadth, the endogenous phage trigger, or exact RloC profile-to-activity mapping. scope_status: NONMECHANISTIC scope_notes: The graph captures RloC as a named DefenseFinder one-profile phage-defense system while leaving natural host breadth, the endogenous DNA-break trigger, phage restriction strength, and RloC profile-to-activity mapping unresolved. nodes: - node_id: rloc_locus label: RloC locus node_type: GENETIC_ELEMENT description: A DefenseFinder RloC phage-defense locus represented by the RloC__RloC profile. - node_id: dna_break_responsive_rloc_activation label: DNA-break-responsive RloC activation node_type: BIOLOGICAL_PROCESS description: Activation of RloC anticodon nuclease activity by double-stranded DNA breaks, causing wobble nucleotide excision from tRNA. - node_id: rloc_system_trait label: RloC system node_type: TRAIT grounding: traitmech:000366 description: Possession of a genome-encoded RloC 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: rloc_locus predicate: contributes to predicate_id: RO:0002326 object: dna_break_responsive_rloc_activation description: RloC encodes a wobble nucleotide-excising anticodon nuclease, Acinetobacter baylyi RloC responds to T4 host DNA degradation when expressed in Escherichia coli, and DefenseFinder models RloC as a one-profile system. evidence: - reference: PMID:18681940 snippet: The conserved bacterial protein RloC, a distant homologue of the tRNA(Lys) anticodon nuclease (ACNase) PrrC, is shown here to act as a wobble nucleotide-excising and Zn(++)-responsive tRNase. notes: Davidov and Kaufmann identify RloC as a wobble nucleotide-excising and zinc-responsive tRNase. - reference: PMID:26031711 snippet: In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks. notes: Bitton et al. support RloC ACNase regulation by an internal double-stranded-DNA-break switch. - reference: PMID:26031711 snippet: Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation. notes: Bitton et al. show T4 host DNA degradation activates Acinetobacter baylyi RloC expressed in Escherichia coli. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'RloC | 10\.1111/j\.1365-2958\.2008\.06387\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase' notes: The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t" notes: The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| RloC__RloC | RloC__RloC | RloC | Custom | 120 |' notes: The DefenseFinder HMM inventory records RloC__RloC under RloC. - subject: dna_break_responsive_rloc_activation predicate: confers predicate_id: METPO:2007700 object: rloc_system_trait description: DNA-break-responsive RloC anticodon nuclease activation realizes the RloC system trait. evidence: - reference: PMID:26031711 snippet: Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation. notes: Bitton et al. show that wild-type phage T4 activates Acinetobacter baylyi RloC expressed in Escherichia coli. - reference: PMID:26031711 snippet: Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction. notes: Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target. - subject: rloc_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: RloC system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: 'RloC | 10\.1111/j\.1365-2958\.2008\.06387\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase' notes: The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "RloC\tRloC\t1\t1\tRloC__RloC\t\t\t" notes: The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile. discussions: - discussion_id: rloc-mechanism-gap prompt: Resolve natural RloC host breadth, endogenous RloC activation triggers, phage restriction strength, and RloC profile-to-activity mapping before minting narrower RloC mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Davidov and Kaufmann support RloC as a bacterial wobble nucleotide-excising tRNase, Bitton et al. show that Acinetobacter baylyi RloC responds to phage T4 host DNA degradation in an Escherichia coli expression context, and DefenseFinder models RloC as a one-profile system with an RloC__RloC marker. Natural host breadth, native phage triggers, restriction strength, and profile-to-activity mapping remain unresolved. evidence: - reference: PMID:26031711 snippet: The natural role of the conserved bacterial anticodon nuclease (ACNase) RloC is not known, but traits that set it apart from the homologous phage T4-excluding ACNase PrrC could provide relevant clues. notes: Bitton et al. leave the natural role of conserved bacterial RloC unknown while comparing it to the phage T4-excluding PrrC ACNase. attaches_to: - causal_graphs#rloc_locus_triggers_dna_break_responsive_activation posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T13:03:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted RloC 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_v243. llm_assisted: true - timestamp: '2026-09-22T13:03:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 'Reviewed the RloC canonical_examples gap and left canonical_examples empty: the current evidence supports RloC as a wobble nucleotide-excising tRNase, T4 activation of Acinetobacter baylyi RloC expressed in Escherichia coli, and the pinned DefenseFinder RloC profile, but does not cite a directly observed natural microbial taxon with a source-backed RloC locus broad enough for a canonical example. No paid research was used.' llm_assisted: true