identifier: traitmech:000446 label: DS-21 system definition: A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 21 locus cataloged as working transcriptional unit TOXO 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-21 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: TOXO synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-21__DS-21A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-21__DS-21B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-21__DS-21C synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md 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: "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein,\ \ hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t\ 2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21" notes: The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t\ 24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "TOXO\tDS-21\tTrue" notes: The final Science supplementary Table S8 maps TOXO to replicated display name DS-21. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "TOXO\t3.0\t211.0\tWP_001557682.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\t\ hhpred_4621019.hhr\t37.0\t160.0\t0.96\t2024-07-29 00:00:00\t121-123\t103.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001557682.1 in TOXO. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-21 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ' notes: The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-21__DS-21A | | DS-21 | Custom | 20 | | DS-21__DS-21B | | DS-21 | Custom | 250 | | DS-21__DS-21C | | DS-21 | Custom | 70 |' notes: 'The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C.' causal_graphs: - graph_id: ds_21_locus_reduces_phage_plaquing title: DS-21 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the three-gene DS-21 locus to reduced bacteriophage plaquing without resolving DS-21 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-21 as the validated TOXO transcriptional unit with three product accessions, a PDDEXK HHpred-domain row, and three DefenseFinder DS-21 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-21 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_21_locus label: DS-21 locus node_type: GENETIC_ELEMENT description: A three-gene DefensePredictor-discovered system 21 locus represented in the pinned DefenseFinder HMM inventory by three DS-21 custom profiles. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage plaquing in cells carrying cloned TOXO. - node_id: ds_21_system_trait label: DS-21 system node_type: TRAIT grounding: traitmech:000446 description: Possession of a genome-encoded DS-21 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_21_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-21/TOXO 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: "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical\ \ protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t\ 10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\t\ DS-21" notes: The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t\ 24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "TOXO\tDS-21\tTrue" notes: The final Science supplementary Table S8 maps TOXO to replicated display name DS-21. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-21__DS-21A | | DS-21 | Custom | 20 | | DS-21__DS-21B | | DS-21 | Custom | 250 | | DS-21__DS-21C | | DS-21 | Custom | 70 |' notes: 'The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C.' - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_21_system_trait description: DS-21-mediated phage plaquing reduction realizes the DS-21 system trait. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical\ \ protein, hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t\ 10.9763556055726\t2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\t\ DS-21" notes: The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t\ 24-07-25\t24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477. - 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 DefensePredictor discovered systems. - subject: ds_21_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-21 system possession is a phage-defense-system trait. 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 DefensePredictor discovered systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-21 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ' notes: The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-21-defensefinder-model-gap prompt: Resolve DS-21 native host breadth, exact profile-to-protein mapping, HHpred-domain interpretation, component chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-21 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-21 as the defensive TOXO transcriptional unit and final Science Tables S6/S7/S8 map it to three product accessions, a Bas1 phage readout, display name DS-21, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records three DS-21 custom profile rows. The pinned rules table has no DS-21 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-21 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: "TOXO\tNZ_QOXJ01000032.1\tGCF_003334085.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t7805\t9963\thypothetical protein, hypothetical protein,\ \ hypothetical protein\tWP_001532221.1, WP_001557682.1, WP_021552536.1\t10.9763556055726\t\ 2.883007179633958\tTrue\tTrue\tPredicted novel defense gene\tDS-21" notes: The final Science supplementary Table S6 maps working_id TOXO to DS_name DS-21, marks the cloned transcriptional unit as defensive, and records NZ_QOXJ01000032.1 positions 7805-9963 with three product accessions. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t3000000\tTOXO\t24-07-25\t\ 24-07-25_PDX1_TMO1_VANC_TOXO.png\t2\t1\t\t100\t4.477121254719663\t\t\tTrue\t\ LB\t37" notes: The final Science supplementary Table S7 reports a TOXO assay row with a Bas1 phage readout and a -log(EOP) value of 4.477. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "TOXO\tDS-21\tTrue" notes: The final Science supplementary Table S8 maps TOXO to replicated display name DS-21. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "TOXO\t3.0\t211.0\tWP_001557682.1\tPDDEXK\tPF18742.6\tDpnII-MboI ; REase_DpnII-MboI\t\ hhpred_4621019.hhr\t37.0\t160.0\t0.96\t2024-07-29 00:00:00\t121-123\t103.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_001557682.1 in TOXO. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-21 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | ' notes: The pinned DefenseFinder article registry maps the DS-21 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-21__DS-21A | | DS-21 | Custom | 20 | | DS-21__DS-21B | | DS-21 | Custom | 250 | | DS-21__DS-21C | | DS-21 | Custom | 70 |' notes: 'The pinned DefenseFinder HMM inventory records three DS-21 custom profiles: DS-21__DS-21A, DS-21__DS-21B, and DS-21__DS-21C.' - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-21, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_21_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T22:17:01Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-21 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 TOXO transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v323 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T22:17:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-21 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned TOXO assays in E. coli MG1655 and DefenseFinder DS-21 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-21 activity. No paid research was used. llm_assisted: true