identifier: traitmech:000429 label: DS-14 system definition: A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 14 locus cataloged as working transcriptional unit RMOR 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-14 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: RMOR synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-14__DS-14 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: "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t\ 14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14" notes: The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t24-07-17\t\ 24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\t\tTrue\t\ LB\t37" notes: The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\tDS-14\tTrue" notes: The final Science supplementary Table S8 maps RMOR to replicated display name DS-14. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\t1.0\t816.0\tWP_040091717.1\tAAA+ ATPase\t7MCA_A\tOrigin recognition\ \ complex subunit 1; replication initiation, REPLICATION; HET: AGS; 3.6A {Saccharomyces\ \ cerevisiae}\thhpred_4983760.hhr\t270.0\t569.0\t0.99\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports an AAA+ ATPase HHpred hit for WP_040091717.1 in RMOR. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\t1.0\t816.0\tWP_040091717.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI\ \ N-terminal domain\thhpred_4983760.hhr\t27.0\t167.0\t0.99\t2024-07-30 00:00:00\t\ 76-78\t65.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_040091717.1 in RMOR. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-14 | 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-14 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-14__DS-14 | | DS-14 | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile. causal_graphs: - graph_id: ds_14_locus_reduces_phage_plaquing title: DS-14 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the single-gene DS-14 locus to reduced bacteriophage plaquing without resolving DS-14 component function or effector activity. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-14 as the validated RMOR transcriptional unit with one product accession and with a DefenseFinder DS-14 profile row. Although Table S6 classes RMOR as a Remote defense homolog, the graph does not assert which defense family it is remote from, native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact AAA+ ATPase or PDDEXK nuclease chemistry, phage target breadth, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_14_locus label: DS-14 locus node_type: GENETIC_ELEMENT description: A single-gene DefensePredictor-discovered system locus represented in the pinned DefenseFinder HMM inventory by one DS-14 custom profile. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing by bacteriophage Bas50 in cells carrying cloned RMOR. - node_id: ds_14_system_trait label: DS-14 system node_type: TRAIT grounding: traitmech:000429 description: Possession of a genome-encoded DS-14 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_14_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-14/RMOR 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: "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t\ 14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\t\ DS-14" notes: The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t\ 24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-14__DS-14 | | DS-14 | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_14_system_trait description: DS-14-mediated phage plaquing reduction realizes the DS-14 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: "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t\ 14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\t\ DS-14" notes: The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t\ 24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699. - subject: ds_14_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-14 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-14 | 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-14 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-14-defensefinder-model-gap prompt: Resolve DS-14 native host breadth, exact single-component activity, DS-14 remote-defense-homolog family identity, DS-14 profile-to-protein mapping, sensitive-phage breadth, exact AAA+ ATPase and PDDEXK nuclease chemistry, and rule-level detection criteria before minting narrower DS-14 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-14 as the defensive RMOR transcriptional unit that reduced Bas50 plaquing when cloned in E. coli MG1655, the final Table S6 classes RMOR as a Remote defense homolog, and the pinned DefenseFinder HMM inventory records one DS-14 profile row. The pinned rules table has no DS-14 row, and the first-pass record does not resolve native host breadth, exact component activity, remote defense family relationship, profile-to-protein mapping, phage target breadth, or endogenous DS-14 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: "RMOR\tNZ_QOZC01000013.1\tGCF_003333475.1\t-\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t106880\t109330\thypothetical protein\tWP_040091717.1\t\ 14.71279098470142\t5.293304824724491\tTrue\tTrue\tRemote defense homolog\tDS-14" notes: The final Science supplementary Table S6 maps working_id RMOR to DS_name DS-14, marks the cloned transcriptional unit as defensive, and records NZ_QOZC01000013.1 positions 106880-109330 with product accession WP_040091717.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas50\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t500000000\tRMOR\t\ 24-07-17\t24-07-17_AAA2_RMOR_NERD_NUCS.png\t3\t10\t\t10000\t4.698970004336019\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an RMOR assay row with a Bas50 phage readout and a -log(EOP) value of 4.699. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\tDS-14\tTrue" notes: The final Science supplementary Table S8 maps RMOR to replicated display name DS-14. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\t1.0\t816.0\tWP_040091717.1\tAAA+ ATPase\t7MCA_A\tOrigin recognition\ \ complex subunit 1; replication initiation, REPLICATION; HET: AGS; 3.6A {Saccharomyces\ \ cerevisiae}\thhpred_4983760.hhr\t270.0\t569.0\t0.99\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports an AAA+ ATPase HHpred hit for WP_040091717.1 in RMOR. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "RMOR\t1.0\t816.0\tWP_040091717.1\tPDDEXK\tPF15516.11\tBpuSI_N ; BpuSI\ \ N-terminal domain\thhpred_4983760.hhr\t27.0\t167.0\t0.99\t2024-07-30 00:00:00\t\ 76-78\t65.0" notes: The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_040091717.1 in RMOR. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-14 | 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-14 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-14__DS-14 | | DS-14 | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records DS-14__DS-14 as a custom DS-14 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-14, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_14_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-28' curation_history: - timestamp: '2026-09-28T08:11:18Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-14 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 RMOR transcriptional-unit level because the pinned DefenseFinder DS-14 HMM row is not backed by a rules row; proposals/metpo_traitmech_v306 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-28T08:11:19Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-14 system canonical_examples and left them empty because DeWeirdt et al. support cloned RMOR plaquing assays in E. coli MG1655 plus a DefenseFinder DS-14 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-14 activity. No paid research was used. llm_assisted: true