identifier: traitmech:000424 label: DS-1 system definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 1 locus cataloged as working transcriptional unit D390 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-1 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: D390 synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-1__DS-1A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-1__DS-1B 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: "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated\ \ protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\t\ True\tFalse\tPredicted novel defense gene\tDS-1" notes: The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\t\ LB\t37" notes: The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "D390\tDS-1\tTrue" notes: The final Science supplementary Table S8 maps D390 to replicated display name DS-1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-1 | 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-1 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-1__DS-1A | | DS-1 | Custom | 30 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-1__DS-1B | | DS-1 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile. causal_graphs: - graph_id: ds_1_locus_reduces_phage_plaquing title: DS-1 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking the two-gene DS-1 locus to reduced bacteriophage plaquing without resolving DS-1 component functions or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-1 as the validated D390 transcriptional unit with two product accessions and with DefenseFinder DS-1A and DS-1B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_1_locus label: DS-1 locus node_type: GENETIC_ELEMENT description: A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-1A and DS-1B custom profiles. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing or reduced plaque size by bacteriophages in cells carrying cloned D390. - node_id: ds_1_system_trait label: DS-1 system node_type: TRAIT grounding: traitmech:000424 description: Possession of a genome-encoded DS-1 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_1_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-1/D390 locus contributes to reduced bacteriophage plaquing when plasmid expressed. 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 validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated\ \ protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\t\ True\tFalse\tPredicted novel defense gene\tDS-1" notes: The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t\ 24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\t\ True\tTrue\t\tLB\t37" notes: The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-1__DS-1A | | DS-1 | Custom | 30 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-1__DS-1B | | DS-1 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_1_system_trait description: DS-1-mediated phage plaquing reduction realizes the DS-1 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 each validated transcriptional unit as a DefensePredictor discovered system. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated\ \ protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\t\ True\tFalse\tPredicted novel defense gene\tDS-1" notes: The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t\ 24-03-12\t24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\t\ True\tTrue\t\tLB\t37" notes: The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602. - subject: ds_1_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-1 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. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-1 | 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-1 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-1-defensefinder-model-gap prompt: Resolve DS-1 native host breadth, exact DS-1A/DS-1B component functions, profile-to-component mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-1 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-1 as the defensive D390 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records DS-1A and DS-1B profile rows. The pinned rules table has no DS-1 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-component mapping, phage target breadth, the direct molecular output, or endogenous DS-1 activity. 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 predicted transcriptional units by measuring plaquing relative to an empty vector control strain. - 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: "D390\tNZ_RRVY01000002.1\tGCF_003886375.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t220602\t222994\thypothetical protein, nucleoid-associated\ \ protein\tWP_000150292.1, WP_000355468.1\t12.74067081596784\t-2.197224577336219\t\ True\tFalse\tPredicted novel defense gene\tDS-1" notes: The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t40000000\tD390\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t7.6020599913279625\tTrue\tTrue\t\ \tLB\t37" notes: The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "D390\tDS-1\tTrue" notes: The final Science supplementary Table S8 maps D390 to replicated display name DS-1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-1 | 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-1 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-1__DS-1A | | DS-1 | Custom | 30 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-1__DS-1B | | DS-1 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-1, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_1_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T02:18:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-1 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 cloned D390 transcriptional unit level because the pinned DefenseFinder DS-1 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v301 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T02:18:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-1 system canonical_examples and left them empty because DeWeirdt et al. support cloned D390 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-1 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-1 activity. No paid research was used. llm_assisted: true - timestamp: '2026-09-28T03:20:08Z' curator: codex action: ADDRESSED_PR_REVIEW changes: Addressed issue 1380 by rewriting the DS-1 definition so D390 is a DeWeirdt et al. working transcriptional-unit identifier rather than an implied E. coli transcriptional unit, expanding the DOI evidence snippets to explicitly state E. coli MG1655 low-copy plasmid expression, and syncing the METPO proposal definition. llm_assisted: true