identifier: traitmech:000525 label: Brc59 system definition: A phage defense system in which an organism possesses a Brc59 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge. definition_source: DOI:10.1126/science.ads0915 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: brc59 synonym_type: RELATED_SYNONYM source: DOI:10.1126/science.ads0915 evidence: - reference: DOI:10.1126/science.ads0915 snippet: brc59 L 44.7 49.6 87.3 98.6 7.6 notes: Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13. - reference: DOI:10.1126/science.ads0915 snippet: brc59 H 12.8 75.8 80.3 60.9 notes: Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13. - reference: DOI:10.1126/science.ads0915 snippet: defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages notes: Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel. - reference: DOI:10.1126/science.ads0915 snippet: 'brc59 brc128 brc135 brc142 brc167.2 brc167' notes: Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures. - reference: https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf snippet: 'C800 pMBA brc59 E. coli IJ1862' notes: Kieffer et al.'s supplementary construct table lists pMBA brc59 in E. coli IJ1862 for high/low-MOI phage-panel testing. - reference: https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf snippet: 'C810 pMBA brc59 K. pneumoniae KP5' notes: Kieffer et al.'s supplementary construct table lists the pMBA brc59 plasmid introduced into Klebsiella pneumoniae KP5. causal_graphs: - graph_id: brc59_integron_cassette_confers_phage_resistance title: Brc59 BRiCs confer phage resistance description: Conservative system-level sketch linking a Brc59 bacteriophage-resistance integron cassette to phage resistance and Brc59 system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures Brc59 at the integron-cassette and phage-resistance-output level without asserting the native host range, exact sensitive-phage breadth outside the reported panels, direct molecular substrate, a normalized gcu59 source key, or a DefenseFinder article/HMM/rules profile absent from the pinned snapshot. nodes: - node_id: brc59_integron_cassette label: Brc59 integron cassette node_type: GENETIC_ELEMENT description: A mobile integron gene cassette curated here as Brc59. - node_id: brc59_phage_resistance label: Brc59 phage resistance node_type: BIOLOGICAL_PROCESS description: Reduced phage inhibition in cells carrying the Brc59 integron cassette. - node_id: brc59_system_trait label: Brc59 system node_type: TRAIT grounding: traitmech:000525 description: Possession of a genome-encoded Brc59 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: brc59_integron_cassette predicate: contributes to predicate_id: RO:0002326 object: brc59_phage_resistance description: The Brc59 integron cassette contributes to phage resistance during phage-panel assays. evidence: - reference: DOI:10.1126/science.ads0915 snippet: brc59 L 44.7 49.6 87.3 98.6 7.6 notes: Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13. - reference: DOI:10.1126/science.ads0915 snippet: brc59 H 12.8 75.8 80.3 60.9 notes: Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13. - subject: brc59_phage_resistance predicate: confers predicate_id: METPO:2007700 object: brc59_system_trait description: Brc59-linked phage resistance realizes the Brc59 system possession trait. evidence: - reference: DOI:10.1126/science.ads0915 snippet: brc59 L 44.7 49.6 87.3 98.6 7.6 notes: Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13. - reference: DOI:10.1126/science.ads0915 snippet: brc59 H 12.8 75.8 80.3 60.9 notes: Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13. - reference: DOI:10.1126/science.ads0915 snippet: defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages notes: Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel. - subject: brc59_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Brc59 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1126/science.ads0915 snippet: defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages notes: Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel. - reference: DOI:10.1126/science.ads0915 snippet: 'brc59 brc128 brc135 brc142 brc167.2 brc167' notes: Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures. discussions: - discussion_id: brc59-defensefinder-model-gap prompt: Resolve Brc59 native host breadth, exact sensitive-phage breadth, molecular output, normalized source-key naming, and DefenseFinder article/HMM/rules coverage before minting narrower Brc59 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Kieffer et al. identify brc59 as a bacteriophage-resistance integron cassette. The pinned DefenseFinder article registry, HMM inventory, and rules table have no exact gcu59 or Brc59 row, so the first-pass record leaves native-host breadth, profile boundaries, exact phage target breadth, direct molecular output, and normalized gcu59 source-key status unresolved. evidence: - reference: DOI:10.1126/science.ads0915 snippet: brc59 L 44.7 49.6 87.3 98.6 7.6 notes: Manual transcription of the Supplementary Fig. S2 Brc59 low-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 44.7% for MS2, 49.6% for T4, 87.3% for F1, 98.6% for T7, and 7.6% for F13. - reference: DOI:10.1126/science.ads0915 snippet: brc59 H 12.8 75.8 80.3 60.9 notes: Manual transcription of the Supplementary Fig. S2 Brc59 high-MOI E. coli IJ1862 heatmap row; the visible cells show reduced inhibition, including 12.8% for MS2, 75.8% for F1, 80.3% for HK544, and 60.9% for F13. - reference: DOI:10.1126/science.ads0915 snippet: defense profiles of identified Bacteriophage Resistance integron Cassettes (BRiCs) against a panel of different phages notes: Kieffer et al. classify positive integron cassettes as BRiCs and compare their defense profiles across a phage panel. - reference: DOI:10.1126/science.ads0915 snippet: 'brc59 brc128 brc135 brc142 brc167.2 brc167' notes: Kieffer et al. include brc59 among identified BRiCs with predicted attC secondary structures. - reference: https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf snippet: 'C800 pMBA brc59 E. coli IJ1862' notes: Kieffer et al.'s supplementary construct table lists pMBA brc59 in E. coli IJ1862 for high/low-MOI phage-panel testing. - reference: https://www.science.org/doi/suppl/10.1126/science.ads0915/suppl_file/science.ads0915_sm.pdf snippet: 'C810 pMBA brc59 K. pneumoniae KP5' notes: Kieffer et al.'s supplementary construct table lists the pMBA brc59 plasmid introduced into Klebsiella pneumoniae KP5. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md notes: A structured first-pass search of the pinned DefenseFinder article registry found no exact gcu59, brc59, or Brc59 row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact gcu59, brc59, or Brc59 row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact gcu59, brc59, or Brc59 system row. attaches_to: - causal_graphs#brc59_integron_cassette_confers_phage_resistance posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T20:28:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Brc59 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review ruled out same-scope live TraitMech, METPO, history, and prior proposal collisions after reviewing exact Brc59/brc59/gcu59 hits; kept the graph at BRiC integron-cassette level because the pinned DefenseFinder article registry, HMM inventory, and rules table have no exact Brc59 row; the replacement placeholder is reserved in proposals/metpo_traitmech_v402. llm_assisted: true - timestamp: '2026-10-01T20:28:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Brc59 system during initial curation and left canonical_examples empty because the sources support heterologous brc59 phage-resistance assays but not a direct named native microbial isolate exemplar with experimentally verified endogenous Brc59 activity. No paid research was used. llm_assisted: true