identifier: traitmech:000471 label: DS-46 system definition: A phage defense system in which an organism possesses the two-gene DS-46 locus cataloged as working transcriptional unit RMRT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing. definition_source: DOI:10.1126/science.adv7924 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: DS-46 synonym_type: EXACT_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: RMRT synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx evidence: - reference: DOI:10.1126/science.adv7924 snippet: To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain notes: DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli. - reference: DOI:10.1126/science.adv7924 snippet: We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. notes: DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\t\ HHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical protein\t\ WP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\tFalse\t\ True\t\tDS-46" notes: The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495. causal_graphs: - graph_id: ds_46_locus_reduces_phage_plaquing title: DS-46 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the two-gene DS-46 locus to reduced bacteriophage plaquing without resolving DS-46 phage-specific readouts, domain annotations, DefenseFinder model coverage, or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-46 as the validated RMRT transcriptional unit with two Table S6 product accessions. It does not assert phage-specific Table S7 readouts, Table S8 display-name rows, Table S8 HHpred-domain rows, DefenseFinder article/HMM/rules rows, native host breadth, exact component activities, molecular output, complete phage breadth, or endogenous DS-46 activity. nodes: - node_id: ds_46_locus label: DS-46 locus node_type: GENETIC_ELEMENT description: A two-gene DS-46 locus cataloged as working transcriptional unit RMRT in final Science supplementary Table S6. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage plaquing in cells carrying cloned RMRT. - node_id: ds_46_system_trait label: DS-46 system node_type: TRAIT grounding: traitmech:000471 description: Possession of a genome-encoded DS-46 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: ds_46_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-46/RMRT locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays. evidence: - reference: DOI:10.1126/science.adv7924 snippet: To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain notes: DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\t\ True\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical\ \ protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\t\ False\tTrue\t\tDS-46" notes: The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_46_system_trait description: DS-46-mediated phage plaquing reduction realizes the DS-46 system trait. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\t\ True\tHHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical\ \ protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\t\ False\tTrue\t\tDS-46" notes: The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495. - reference: DOI:10.1126/science.adv7924 snippet: We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. notes: The DS nomenclature is used for validated phage-defense transcriptional units. - subject: ds_46_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-46 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1126/science.adv7924 snippet: To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain notes: DeWeirdt et al. validate DSs as anti-phage systems. discussions: - discussion_id: ds-46-model-coverage-gap prompt: Resolve DS-46 phage-specific readouts, display-name and domain rows, DefenseFinder model coverage, native host breadth, exact component activities, molecular output, complete phage breadth, and endogenous activity before minting narrower DS-46 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-46 as the defensive RMRT transcriptional unit and final Science Table S6 maps RMRT to two product accessions. A first-pass final Science Table S7/S8 review found no exact RMRT/DS-46 phage-specific readout, display-name row, or HHpred-domain row. The pinned DefenseFinder article, HMM, and rules registries also do not list DS-46 or RMRT, and the first-pass record therefore does not resolve native host breadth, complete phage breadth, exact component activities, molecular output, or endogenous DS-46 activity. evidence: - reference: DOI:10.1126/science.adv7924 snippet: We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. notes: DeWeirdt et al. name validated TUs as DSs. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "RMRT\tNZ_RRVG01000021.1\tGCF_003886135.1\t+\tFalse\tFalse\tTrue\tTrue\t\ HHblits hits\t62985\t63495\tDUF3606 domain-containing protein, hypothetical\ \ protein\tWP_001406733.1, WP_000002748.1\t-4.513359272522268\t5.517452896464706\t\ False\tTrue\t\tDS-46" notes: The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx notes: A structured first-pass search of final Science supplementary Table S7 found no exact RMRT or DS-46 system row to connect DS-46 to a phage-specific readout. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx notes: A structured first-pass search of final Science supplementary Table S8 found no exact RMRT or DS-46 display-name or HHpred-domain row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md notes: The pinned DefenseFinder article registry has no exact DS-46 or RMRT row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: The pinned DefenseFinder HMM inventory has no exact DS-46 or RMRT profile row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table has no exact DS-46 or RMRT model row. attaches_to: - causal_graphs#ds_46_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T18:46:02Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-46 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; kept the graph at RMRT transcriptional-unit level because phage-specific Table S7 readouts, Table S8 display and domain rows, DefenseFinder article/HMM/rules coverage, native host breadth, exact component activities, complete phage breadth, and molecular output remain unresolved, and proposals/metpo_traitmech_v348 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-29T18:46:03Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-46 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RMRT assays in E. coli MG1655, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-46 activity. No paid research was used. llm_assisted: true