identifier: traitmech:000427 label: DS-4 system definition: A phage defense system in which an organism possesses the five-gene DefensePredictor-discovered system 4 locus cataloged as working transcriptional unit NTTI 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-4 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: NTTI synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-4__DS-4A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-4__DS-4B synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-4__DS-4C synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-4__DS-4D synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-4__DS-4E 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: "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase, putative\ \ DNA base hypermodification protein, TIR domain-containing protein, hypothetical\ \ protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, WP_047174762.1\t\ 8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted novel defense gene\t\ DS-4" notes: The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t24-03-12\t\ 24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\tTrue\t\ True\t\tLB\t37" notes: The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "NTTI\tDS-4\tTrue" notes: The final Science supplementary Table S8 maps NTTI to replicated display name DS-4. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-4 | 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-4 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-4__DS-4A | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4B | | DS-4 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4C | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4D | | DS-4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4E | | DS-4 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile. causal_graphs: - graph_id: ds_4_locus_reduces_phage_plaquing title: DS-4 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the five-gene DS-4 locus to reduced bacteriophage plaquing without resolving DS-4 component functions or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-4 as the validated NTTI transcriptional unit with five product accessions and with DefenseFinder DS-4A, DS-4B, DS-4C, DS-4D, and DS-4E 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_4_locus label: DS-4 locus node_type: GENETIC_ELEMENT description: A five-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-4A, DS-4B, DS-4C, DS-4D, and DS-4E 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 NTTI. - node_id: ds_4_system_trait label: DS-4 system node_type: TRAIT grounding: traitmech:000427 description: Possession of a genome-encoded DS-4 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_4_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-4/NTTI 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: "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase,\ \ putative DNA base hypermodification protein, TIR domain-containing protein,\ \ hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1,\ \ WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted\ \ novel defense gene\tDS-4" notes: The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t\ 24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\t\ True\tTrue\t\tLB\t37" notes: The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4A | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4B | | DS-4 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4C | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4D | | DS-4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4E | | DS-4 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_4_system_trait description: DS-4-mediated phage plaquing reduction realizes the DS-4 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: "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase,\ \ putative DNA base hypermodification protein, TIR domain-containing protein,\ \ hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1,\ \ WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted\ \ novel defense gene\tDS-4" notes: The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t\ 24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\t\ True\tTrue\t\tLB\t37" notes: The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933. - subject: ds_4_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-4 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-4 | 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-4 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-4-defensefinder-model-gap prompt: Resolve DS-4 native host breadth, exact five-component activities, DS-4 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-4 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-4 as the defensive NTTI transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records five DS-4 profile rows. The pinned rules table has no DS-4 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-protein mapping, phage target breadth, or endogenous DS-4 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: "NTTI\tNZ_QOYB01000018.1\tGCF_003333785.1\t+\tTrue\tFalse\tTrue\tTrue\t\ DefensePredictor hits\t32107\t36002\tthymidylate synthase, adenylate kinase,\ \ putative DNA base hypermodification protein, TIR domain-containing protein,\ \ hypothetical protein\tWP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1,\ \ WP_047174762.1\t8.47705415994386\t4.820281565605036\tTrue\tTrue\tPredicted\ \ novel defense gene\tDS-4" notes: The final Science supplementary Table S6 maps working_id NTTI to DS_name DS-4, marks the cloned transcriptional unit as defensive, and records NZ_QOYB01000018.1 positions 32107-36002 with product accessions WP_087900468.1, WP_087900469.1, WP_087900470.1, WP_072044445.1, and WP_047174762.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Lambda\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t60000000\tNTTI\t\ 24-03-12\t24-03-12_NTTI_PN12_SVIR_D390.png\t6\t7\tY\t7000000\t0.9330532103693868\t\ True\tTrue\t\tLB\t37" notes: The final Science supplementary Table S7 reports an NTTI assay row with a lambda phage readout, smaller plaque size marked Y, and a -log(EOP) value of 0.933. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "NTTI\tDS-4\tTrue" notes: The final Science supplementary Table S8 maps NTTI to replicated display name DS-4. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-4 | 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-4 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-4__DS-4A | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4A as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4B | | DS-4 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4B as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4C | | DS-4 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4C as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4D | | DS-4 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4D as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-4__DS-4E | | DS-4 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-4__DS-4E as a custom DS-4 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-4, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_4_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T06:12:08Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-4 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 NTTI transcriptional-unit level because the pinned DefenseFinder DS-4 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v304 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T06:12:09Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-4 system canonical_examples and left them empty because DeWeirdt et al. support cloned NTTI plaquing assays in E. coli MG1655 plus a DefenseFinder DS-4 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-4 activity. No paid research was used. llm_assisted: true