identifier: traitmech:000433 label: DS-9 system definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 9 locus cataloged with working_id MHAD 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-9 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: MHAD synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-9__DS-9A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-9__DS-9B 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: The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase notes: DeWeirdt et al. identify DS-9 as a two-gene system with metallophosphatase and HAD phosphatase domains. - reference: DOI:10.1126/science.adv7924 snippet: When we mutated the predicted catalytic residues in the metallophosphatase domain of DS-9A, we saw a loss of defense, suggesting it is essential for protection notes: DeWeirdt et al. report that predicted DS-9A metallophosphatase catalytic-residue mutations caused a loss of defense. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\t\ WP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\tTrue\t\ Predicted novel defense gene\tDS-9" notes: The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1. - 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\tMHAD\t24-03-08\t\ 24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\tLB\t\ 37" notes: The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\t\ MHAD\t\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t2\t\ 8\t\t800\t3.574031268" notes: The final Science supplementary Table S7 reports the MHAD WT Bas1 mutant-panel row with a -log(EOP) value of 3.574. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\t\ MHAD\tD207A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t\ 6\t3\t\t3000000\t0" notes: The final Science supplementary Table S7 reports the MHAD D207A Bas1 mutant-panel row with a -log(EOP) value of 0. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t3000000\t\ MHAD\tN292A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t\ 6\t2\t\t2000000\t0.1760912591" notes: The final Science supplementary Table S7 reports the MHAD N292A Bas1 mutant-panel row with a -log(EOP) value of 0.176. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\tDS-9\tTrue" notes: The final Science supplementary Table S8 maps MHAD to replicated display name DS-9. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\t2.0\t278.0\tWP_000770925.1\tHAD phosphatase\tcd02616\tHAD_PPase;\ \ pyrophosphatase\thhpred_3345609.hhr\t1.0\t277.0\t0.999\t2024-04-16 00:00:00" notes: The final Science supplementary Table S8 reports a HAD phosphatase HHpred hit for WP_000770925.1 in MHAD. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\t1.0\t549.0\tWP_000665639.1\tMetallophosphatase\tcd07378\tMPP_ACP5;\ \ Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain.\t\ hhpred_3407490.hhr\t200.0\t533.0\t0.9983\t2024-04-16 00:00:00" notes: The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_000665639.1 in MHAD. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-9 | 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-9 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-9__DS-9A | | DS-9 | Custom | 300 |' notes: The pinned DefenseFinder HMM inventory records DS-9__DS-9A as a custom DS-9 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-9__DS-9B | | DS-9 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-9__DS-9B as a custom DS-9 profile. causal_graphs: - graph_id: ds_9_locus_reduces_phage_plaquing title: DS-9 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the two-gene DS-9 locus to reduced bacteriophage plaquing without resolving DS-9 component functions or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-9 as the validated MHAD transcriptional unit with two product accessions and with DefenseFinder DS-9A and DS-9B profile rows. It does not assert native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, the direct viral trigger or metallophosphoesterase substrate, the HAD phosphatase target, phage target breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_9_locus label: DS-9 locus node_type: GENETIC_ELEMENT description: A two-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by DS-9A and DS-9B custom profiles. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing by bacteriophage Bas1 in cells carrying cloned MHAD. - node_id: ds_9_system_trait label: DS-9 system node_type: TRAIT grounding: traitmech:000433 description: Possession of a genome-encoded DS-9 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_9_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-9/MHAD locus contributes to reduced bacteriophage plaquing when plasmid expressed. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\t\ WP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\t\ True\tPredicted novel defense gene\tDS-9" notes: The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1. - 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\tMHAD\t\ 24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\t\ True\t\t\tLB\t37" notes: The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_9_system_trait description: DS-9-mediated phage plaquing reduction realizes the DS-9 system trait. evidence: - reference: DOI:10.1126/science.adv7924 snippet: The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase notes: DeWeirdt et al. identify DS-9 as a two-gene metallophosphatase/HAD-phosphatase system. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\t\ WP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\t\ True\tPredicted novel defense gene\tDS-9" notes: The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1. - 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\tMHAD\t\ 24-03-08\t24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\t\ True\t\t\tLB\t37" notes: The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125. - subject: ds_9_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-9 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-9 | 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-9 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-9-defensefinder-model-gap prompt: Resolve DS-9 native host breadth, DS-9A/DS-9B profile-to-protein mapping, sensitive-phage breadth, direct metallophosphoesterase substrate, HAD phosphatase target, and rule-level detection criteria before minting narrower DS-9 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-9 as the defensive MHAD transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, identify DS-9 as a two-gene system with metallophosphatase and HAD phosphatase domains, and report that DS-9A predicted catalytic-residue mutations caused a loss of defense. Final Science Table S7 mutant rows show D207A and N292A Bas1 protection loss relative to wild-type MHAD in a matched panel. The pinned DefenseFinder HMM inventory records two DS-9 profile rows. The pinned rules table has no DS-9 row, and the first-pass record does not resolve native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, direct metallophosphoesterase substrate, HAD phosphatase target, phage target breadth, endogenous DS-9 activity, or DefenseFinder rule-level detection criteria. 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: The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase notes: DeWeirdt et al. identify DS-9 as a two-gene system. - reference: DOI:10.1126/science.adv7924 snippet: When we mutated the predicted catalytic residues in the metallophosphatase domain of DS-9A, we saw a loss of defense, suggesting it is essential for protection notes: DeWeirdt et al. state that DS-9A metallophosphatase catalytic mutants lose defense. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "MHAD\tNZ_QOWZ01000056.1\tGCF_003334705.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t6224\t8706\tHAD-IA family hydrolase, metallophosphoesterase\t\ WP_000770925.1, WP_000665639.1\t4.506698206217075\t6.906754778648663\tTrue\t\ True\tPredicted novel defense gene\tDS-9" notes: The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1. - 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\tMHAD\t24-03-08\t\ 24-03-08_NYND_GHOS_MHAD_UDNG.png\t3\t3\t\t3000\t4.1249387366083\tTrue\t\t\t\ LB\t37" notes: The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\ 3000000\tMHAD\t\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t\ 2\t8\t\t800\t3.574031268" notes: The final Science supplementary Table S7 reports the MHAD WT Bas1 mutant-panel row with a -log(EOP) value of 3.574. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\ 3000000\tMHAD\tD207A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t\ 6\t3\t\t3000000\t0" notes: The final Science supplementary Table S7 reports the MHAD D207A Bas1 mutant-panel row with a -log(EOP) value of 0. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas1\tA.1\tMG1655\t24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png\t\ 3000000\tMHAD\tN292A\t24-07-17\t24-07-17_PN12-dACR_PN12_MHAD_MHAD-D207A_MHAD-N292A.png\t\ 6\t2\t\t2000000\t0.1760912591" notes: The final Science supplementary Table S7 reports the MHAD N292A Bas1 mutant-panel row with a -log(EOP) value of 0.176. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\tDS-9\tTrue" notes: The final Science supplementary Table S8 maps MHAD to replicated display name DS-9. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\t2.0\t278.0\tWP_000770925.1\tHAD phosphatase\tcd02616\tHAD_PPase;\ \ pyrophosphatase\thhpred_3345609.hhr\t1.0\t277.0\t0.999\t2024-04-16 00:00:00" notes: The final Science supplementary Table S8 reports a HAD phosphatase HHpred hit for WP_000770925.1 in MHAD. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "MHAD\t1.0\t549.0\tWP_000665639.1\tMetallophosphatase\tcd07378\tMPP_ACP5;\ \ Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain.\t\ hhpred_3407490.hhr\t200.0\t533.0\t0.9983\t2024-04-16 00:00:00" notes: The final Science supplementary Table S8 reports a metallophosphatase HHpred hit for WP_000665639.1 in MHAD. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-9 | 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-9 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-9__DS-9A | | DS-9 | Custom | 300 |' notes: The pinned DefenseFinder HMM inventory records DS-9__DS-9A as a custom DS-9 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-9__DS-9B | | DS-9 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-9__DS-9B as a custom DS-9 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-9, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_9_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T12:06:48Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-9 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 MHAD transcriptional-unit level because the DS-9A/DS-9B profile-to-protein mapping and rule-level DefenseFinder model remain unresolved; proposals/metpo_traitmech_v310 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T12:06:49Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-9 system canonical_examples and left them empty because DeWeirdt et al. support cloned MHAD plaquing assays in E. coli MG1655 plus DefenseFinder DS-9 model rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-9 activity. No paid research was used. llm_assisted: true