identifier: traitmech:000426 label: DS-3 system definition: A phage defense system in which an organism possesses the one-gene DefensePredictor-discovered system 3 locus cataloged as working transcriptional unit PIN8 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-3 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: PIN8 synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-3__DS-3 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: DOI:10.1126/science.adv7924 snippet: DS-3 is a one-protein system with a PIN ribonuclease domain split between its N and C-terminus notes: DeWeirdt et al. describe DS-3 as a one-protein PIN ribonuclease-domain system. - reference: DOI:10.1126/science.adv7924 snippet: When we mutated catalytic residues in DS-3, the system no longer defended against phage, suggesting this domain is essential for protection. notes: DeWeirdt et al. report that mutating predicted catalytic residues removed DS-3-mediated phage defense. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t\ 8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense gene\t\ DS-3" notes: The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\tLB\t\ 37" notes: The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "PIN8\tDS-3\tTrue" notes: The final Science supplementary Table S8 maps PIN8 to replicated display name DS-3. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-3 | 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-3 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-3__DS-3 | | DS-3 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile. causal_graphs: - graph_id: ds_3_locus_reduces_phage_plaquing title: DS-3 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the one-gene DS-3 locus to reduced bacteriophage plaquing without resolving DS-3 effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-3 as the validated PIN8 transcriptional unit with one product accession and with a DefenseFinder DS-3 profile row. 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_3_locus label: DS-3 locus node_type: GENETIC_ELEMENT description: A one-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by a custom DS-3 profile. - 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 PIN8. - node_id: ds_3_system_trait label: DS-3 system node_type: TRAIT grounding: traitmech:000426 description: Possession of a genome-encoded DS-3 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_3_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-3/PIN8 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: DOI:10.1126/science.adv7924 snippet: When we mutated catalytic residues in DS-3, the system no longer defended against phage, suggesting this domain is essential for protection. notes: DeWeirdt et al. show DS-3 protection depends on predicted catalytic residues. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t\ 8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense\ \ gene\tDS-3" notes: The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\t\ LB\t37" notes: The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-3__DS-3 | | DS-3 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_3_system_trait description: DS-3-mediated phage plaquing reduction realizes the DS-3 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: "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t\ 8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense\ \ gene\tDS-3" notes: The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\t\ LB\t37" notes: The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602. - subject: ds_3_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-3 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-3 | 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-3 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-3-defensefinder-model-gap prompt: Resolve DS-3 native host breadth, exact PIN ribonuclease activity, DS-3 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-3 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-3 as the defensive PIN8 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records a DS-3 profile row. The pinned rules table has no DS-3 row, and the first-pass record does not resolve native host breadth, exact PIN substrate or output, profile-to-protein mapping, phage target breadth, or endogenous DS-3 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: DOI:10.1126/science.adv7924 snippet: DS-3 is a one-protein system with a PIN ribonuclease domain split between its N and C-terminus notes: DeWeirdt et al. report a split PIN ribonuclease domain in the one-protein DS-3 system. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "PIN8\tNZ_RRWT01000005.1\tGCF_003892645.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t244326\t245348\thypothetical protein\tWP_022645725.1\t\ 8.909458355458062\t-2.350827761940385\tTrue\tFalse\tPredicted novel defense\ \ gene\tDS-3" notes: The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "RB69\t1.1\tpLAND\t24-03-08_NYND_PIN2_MHAD_EV.png\t400000\tPIN8\t24-03-12\t\ 24-03-12_PIN8_D390_NADR_PN12.png\t0\t1\t\t1\t5.6020599913279625\tTrue\t\t\t\ LB\t37" notes: The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "PIN8\tDS-3\tTrue" notes: The final Science supplementary Table S8 maps PIN8 to replicated display name DS-3. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-3 | 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-3 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-3__DS-3 | | DS-3 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-3, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_3_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T05:06:03Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-3 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 PIN8 transcriptional-unit level because the pinned DefenseFinder DS-3 HMM row is not backed by a rules row; proposals/metpo_traitmech_v303 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T05:06:04Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-3 system canonical_examples and left them empty because DeWeirdt et al. support cloned PIN8 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-3 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-3 activity. No paid research was used. llm_assisted: true