identifier: traitmech:000428 label: DS-5 system definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 5 locus cataloged as working transcriptional unit PN12 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-5 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: PN12 synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-5__DS-5A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-5__DS-5B 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-5 is a two protein system that also features a PIN ribonuclease, though not closely related to that of DS-3, along with a second protein containing a DUF5830 and a domain homologous to the anti-CRISPR protein AcrIF4 notes: DeWeirdt et al. describe DS-5 as a two-protein system containing PIN, DUF5830, and AcrIF4-like domains. - reference: DOI:10.1126/science.adv7924 snippet: Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense notes: DeWeirdt et al. report that DS-5 phage defense requires the predicted PIN catalytic residues and the AcrIF4-domain-containing gene. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing\ \ protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\t\ True\tFalse\tPredicted novel defense gene\tDS-5" notes: The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t\ 24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\t\ \tLB\t37" notes: The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "PN12\tDS-5\tTrue" notes: The final Science supplementary Table S8 maps PN12 to replicated display name DS-5. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-5 | 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-5 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-5__DS-5A | | DS-5 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-5__DS-5B | | DS-5 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile. causal_graphs: - graph_id: ds_5_locus_reduces_phage_plaquing title: DS-5 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the two-gene DS-5 locus to reduced bacteriophage plaquing without resolving DS-5 component functions or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-5 as the validated PN12 transcriptional unit with two product accessions and with DefenseFinder DS-5A and DS-5B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact PIN-family target, AcrIF4-like component activity, phage target breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_5_locus label: DS-5 locus node_type: GENETIC_ELEMENT description: A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-5A and DS-5B custom profiles. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing by bacteriophage Bas60 in cells carrying cloned PN12. - node_id: ds_5_system_trait label: DS-5 system node_type: TRAIT grounding: traitmech:000428 description: Possession of a genome-encoded DS-5 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_5_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-5/PN12 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: Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense notes: DeWeirdt et al. show that DS-5 protection requires both the predicted PIN catalytic residues and the AcrIF4-domain-containing gene. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing\ \ protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\t\ True\tFalse\tPredicted novel defense gene\tDS-5" notes: The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t\ 24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\t\ True\t\t\tLB\t37" notes: The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-5__DS-5A | | DS-5 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-5__DS-5B | | DS-5 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_5_system_trait description: DS-5-mediated phage plaquing reduction realizes the DS-5 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: "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing\ \ protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\t\ True\tFalse\tPredicted novel defense gene\tDS-5" notes: The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t\ 24-03-09\t24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\t\ True\t\t\tLB\t37" notes: The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699. - subject: ds_5_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-5 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-5 | 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-5 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-5-defensefinder-model-gap prompt: Resolve DS-5 native host breadth, exact two-component activities, DS-5 profile-to-protein mapping, sensitive-phage breadth, DS-5 PIN nuclease target, AcrIF4-like component function, and rule-level detection criteria before minting narrower DS-5 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-5 as the defensive PN12 transcriptional unit that reduced Bas60 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records two DS-5 profile rows. The pinned rules table has no DS-5 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-5 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: DS-5 is a two protein system that also features a PIN ribonuclease, though not closely related to that of DS-3, along with a second protein containing a DUF5830 and a domain homologous to the anti-CRISPR protein AcrIF4 notes: DeWeirdt et al. identify DS-5 as a two-protein system with PIN, DUF5830, and AcrIF4-like domains. - reference: DOI:10.1126/science.adv7924 snippet: Mutating the catalytic residues in the PIN domain eliminated defense. Deleting the AcrIF4 domain-containing gene also ablated defense by DS-5 but did not lead to unrestrained toxicity of the ribonuclease indicating that DS-5 is likely not a TA system and that both components are essential to defense notes: DeWeirdt et al. show that DS-5 phage defense requires both proteins. - 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: "PN12\tNZ_QOYG01000008.1\tGCF_003333715.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t68231\t69878\thypothetical protein, PIN domain-containing\ \ protein\tWP_021513008.1, WP_021513009.1\t10.04757221593433\t-2.824774475410352\t\ True\tFalse\tPredicted novel defense gene\tDS-5" notes: The final Science supplementary Table S6 maps working_id PN12 to DS_name DS-5, marks the cloned transcriptional unit as defensive, and records NZ_QOYG01000008.1 positions 68231-69878 with product accessions WP_021513008.1 and WP_021513009.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t5000000\tPN12\t24-03-09\t\ 24-03-09_NTTI_SVIR_PN12_PIN8.png\t1\t100\t\t1000\t3.6989700043360187\tTrue\t\ \t\tLB\t37" notes: The final Science supplementary Table S7 reports a PN12 assay row with a Bas60 phage readout and a -log(EOP) value of 3.699. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "PN12\tDS-5\tTrue" notes: The final Science supplementary Table S8 maps PN12 to replicated display name DS-5. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-5 | 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-5 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-5__DS-5A | | DS-5 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5A as a custom DS-5 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-5__DS-5B | | DS-5 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-5__DS-5B as a custom DS-5 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-5, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_5_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T07:02:46Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-5 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 PN12 transcriptional-unit level because the pinned DefenseFinder DS-5 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v305 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T07:02:47Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-5 system canonical_examples and left them empty because DeWeirdt et al. support cloned PN12 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-5 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-5 activity. No paid research was used. llm_assisted: true - timestamp: '2026-09-28T07:38:24Z' curator: codex action: FIX_REVIEW_NOTE changes: Reworded the DS-5 mutation evidence note after Claude Code Review issue 1387 so it cites the AcrIF4-domain-containing gene rather than asserting a first-gene ordering that the source text and nonmechanistic graph do not establish. llm_assisted: true