identifier: traitmech:000468 label: DS-43 system definition: A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 43 locus cataloged as working transcriptional unit D668 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-43 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: D668 synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-43__DS-43 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: "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t\ 0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43" notes: The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1. - 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\tD668\t24-07-19\t\ 24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 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_S7.xlsx snippet: "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t\ 24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "D668\tDS-43\tTrue" notes: The final Science supplementary Table S8 maps D668 to replicated display name DS-43. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-43 | 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-43 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-43__DS-43 | | DS-43 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile. causal_graphs: - graph_id: ds_43_locus_reduces_phage_plaquing title: DS-43 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the single-gene DS-43 locus to reduced bacteriophage plaquing without resolving DS-43 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-43 as the validated D668 transcriptional unit with one product accession and one DefenseFinder DS-43 profile row. It does not assert exact profile-to-protein correspondence, native host breadth, DS-43 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_43_locus label: DS-43 locus node_type: GENETIC_ELEMENT description: A single-gene DefensePredictor-discovered system 43 locus represented in the pinned DefenseFinder HMM inventory by one DS-43 custom profile. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage plaquing in cells carrying cloned D668. - node_id: ds_43_system_trait label: DS-43 system node_type: TRAIT grounding: traitmech:000468 description: Possession of a genome-encoded DS-43 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_43_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-43/D668 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: "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t\ 4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\t\ DS-43" notes: The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1. - 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\tD668\t\ 24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 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_S7.xlsx snippet: "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\t\ D668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "D668\tDS-43\tTrue" notes: The final Science supplementary Table S8 maps D668 to replicated display name DS-43. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-43__DS-43 | | DS-43 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_43_system_trait description: DS-43-mediated phage plaquing reduction realizes the DS-43 system trait. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t\ 4.944206899546769\t0.2289954698821485\tTrue\tTrue\tStructural defense homolog\t\ DS-43" notes: The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1. - 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\tD668\t\ 24-07-19\t24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 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_S7.xlsx snippet: "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\t\ D668\t24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114. - 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_43_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-43 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-43 | 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-43 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-43-defensefinder-model-gap prompt: Resolve DS-43 native host breadth, exact component activity, profile-to-protein mapping, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-43 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-43 as the defensive D668 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas19 and SECphi18 phage readouts, and display name DS-43. The pinned DefenseFinder HMM inventory records one DS-43 custom profile row. The pinned rules table has no DS-43 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous DS-43 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: "D668\tNZ_QOYT01000001.1\tGCF_003333565.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t7759\t8424\thypothetical protein\tWP_001057122.1\t4.944206899546769\t\ 0.2289954698821485\tTrue\tTrue\tStructural defense homolog\tDS-43" notes: The final Science supplementary Table S6 maps working_id D668 to DS_name DS-43, marks the cloned transcriptional unit as defensive, and records NZ_QOYT01000001.1 positions 7759-8424 with product accession WP_001057122.1. - 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\tD668\t24-07-19\t\ 24-07-19_D668_RMAP_HJRS_GBPR.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 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_S7.xlsx snippet: "SECphi18\t6.2\tpLAND\t24-07-17_AAA2_VPUS_VAME_EV.png\t1300000000\tD668\t\ 24-07-19\t24-07-19_RMAP_D668_HJRS_ZAPB.png\t3\t10\t\t10000\t5.113943352306837\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 Systems sheet reports a D668 assay row with a SECphi18 phage readout and a -log(EOP) value of 5.114. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "D668\tDS-43\tTrue" notes: The final Science supplementary Table S8 maps D668 to replicated display name DS-43. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-43 | 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-43 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-43__DS-43 | | DS-43 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-43__DS-43 as a custom DS-43 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-43, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_43_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T16:06:36Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-43 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 D668 transcriptional-unit level because component activity and rule rows remain unresolved, and proposals/metpo_traitmech_v345 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-29T16:06:37Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-43 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned D668 assays in E. coli MG1655 and a DefenseFinder DS-43 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-43 activity. No paid research was used. llm_assisted: true