identifier: traitmech:000448 label: DS-23 system definition: A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 23 locus cataloged as working transcriptional unit E2DP 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-23 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: E2DP synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-23__DS-23 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: "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\t\ WP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted novel\ \ defense gene\tDS-23" notes: The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t\ 24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\tDS-23\tTrue" notes: The final Science supplementary Table S8 maps E2DP to replicated display name DS-23. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\t1.0\t719.0\tWP_020231147.1\tZF\t2I9W_A\tHypothetical protein; Cystatin-like\ \ fold, sec-c motif fold, structural genomics\thhpred_7846250.hhr\t693.0\t716.0\t\ 0.98\t2024-07-30 00:00:00\t\t" notes: The final Science supplementary Table S8 reports a ZF HHpred hit for WP_020231147.1 in E2DP. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\t1.0\t719.0\tWP_020231147.1\tPDDEXK\tcd22364\tVC1899-like; putative\ \ nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative\ \ nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs\ \ to a superfamily of PDDEXK nucleases\thhpred_7846250.hhr\t295.0\t457.0\t0.96\t\ 2024-07-30 00:00:00\t110-112\t96.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_020231147.1 in E2DP. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-23 | 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-23 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-23__DS-23 | | DS-23 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile. causal_graphs: - graph_id: ds_23_locus_reduces_phage_plaquing title: DS-23 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the single-gene DS-23 locus to reduced bacteriophage plaquing without resolving DS-23 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-23 as the validated E2DP transcriptional unit with one product accession, ZF and PDDEXK HHpred-domain rows, and one DefenseFinder DS-23 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-23 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_23_locus label: DS-23 locus node_type: GENETIC_ELEMENT description: A single-gene DefensePredictor-discovered system 23 locus represented in the pinned DefenseFinder HMM inventory by one DS-23 custom profile. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage plaquing in cells carrying cloned E2DP. - node_id: ds_23_system_trait label: DS-23 system node_type: TRAIT grounding: traitmech:000448 description: Possession of a genome-encoded DS-23 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_23_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-23/E2DP 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: "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing\ \ protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\t\ Predicted novel defense gene\tDS-23" notes: The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t\ 24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\tDS-23\tTrue" notes: The final Science supplementary Table S8 maps E2DP to replicated display name DS-23. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-23__DS-23 | | DS-23 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_23_system_trait description: DS-23-mediated phage plaquing reduction realizes the DS-23 system trait. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing\ \ protein\tWP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\t\ Predicted novel defense gene\tDS-23" notes: The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t\ 24-07-24\t24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342. - 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_23_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-23 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-23 | 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-23 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-23-defensefinder-model-gap prompt: Resolve DS-23 native host breadth, exact single-component activity, profile-to-protein mapping, ZF and PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-23 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-23 as the defensive E2DP transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_020231147.1, a Bas19 phage readout, display name DS-23, and ZF and PDDEXK HHpred rows. The pinned DefenseFinder HMM inventory records one DS-23 custom profile row. The pinned rules table has no DS-23 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, ZF or PDDEXK activity, molecular output, or endogenous DS-23 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: "E2DP\tNZ_RRVV01000032.1\tGCF_003886345.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t38754\t40913\tSEC-C metal-binding domain-containing protein\t\ WP_020231147.1\t11.17818080568115\t3.842009204807092\tTrue\tTrue\tPredicted\ \ novel defense gene\tDS-23" notes: The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tE2DP\t24-07-24\t\ 24-07-24_ABIL_E2DP_COAT_DDML.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 reports an E2DP assay row with a Bas19 phage readout and a -log(EOP) value of 6.342. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\tDS-23\tTrue" notes: The final Science supplementary Table S8 maps E2DP to replicated display name DS-23. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\t1.0\t719.0\tWP_020231147.1\tZF\t2I9W_A\tHypothetical protein;\ \ Cystatin-like fold, sec-c motif fold, structural genomics\thhpred_7846250.hhr\t\ 693.0\t716.0\t0.98\t2024-07-30 00:00:00\t\t" notes: The final Science supplementary Table S8 reports a ZF HHpred hit for WP_020231147.1 in E2DP. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "E2DP\t1.0\t719.0\tWP_020231147.1\tPDDEXK\tcd22364\tVC1899-like; putative\ \ nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative\ \ nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs\ \ to a superfamily of PDDEXK nucleases\thhpred_7846250.hhr\t295.0\t457.0\t0.96\t\ 2024-07-30 00:00:00\t110-112\t96.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_020231147.1 in E2DP. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-23 | 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-23 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-23__DS-23 | | DS-23 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-23, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_23_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T00:59:43Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-23 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 E2DP transcriptional-unit level because ZF and PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v325 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-29T00:59:44Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-23 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned E2DP assays in E. coli MG1655 and a DefenseFinder DS-23 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-23 activity. No paid research was used. llm_assisted: true