identifier: traitmech:000452 label: DS-28 system definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 28 locus cataloged as working transcriptional unit ANEX 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-28 synonym_type: EXACT_SYNONYM source: DOI:10.1126/science.adv7924 - synonym_text: ANEX synonym_type: RELATED_SYNONYM source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx - synonym_text: DS-28__DS-28A synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DS-28__DS-28B 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: "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\t\ WP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\tTrue\t\ Predicted novel defense gene\tDS-28" notes: The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t\ 24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\tLB\t\ 37" notes: The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\tDS-28\tTrue" notes: The final Science supplementary Table S8 maps ANEX to replicated display name DS-28. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN\ \ pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription\ \ termination, anti-termination, RNAP clamp, phage, transcription initiation,\ \ P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t143.0\t\ 178.0\t0.326\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-28 | 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-28 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-28__DS-28A | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-28__DS-28B | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile. causal_graphs: - graph_id: ds_28_locus_reduces_phage_plaquing title: DS-28 locus reduces bacteriophage plaquing description: Conservative system-level sketch linking the two-gene DS-28 locus to reduced bacteriophage plaquing without resolving DS-28 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures DS-28 as the validated ANEX transcriptional unit with two product accessions, one high-probability HEPN HHpred-domain row, one lower-probability TF HHpred-domain row, and two DefenseFinder DS-28 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-28 molecular activity, trigger, substrate, complete phage breadth, HEPN or transcription-factor HHpred-domain interpretation, or DefenseFinder rule-level detection criteria. nodes: - node_id: ds_28_locus label: DS-28 locus node_type: GENETIC_ELEMENT description: A two-gene DefensePredictor-discovered system 28 locus represented in the pinned DefenseFinder HMM inventory by two DS-28 custom profiles. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage plaquing in cells carrying cloned ANEX. - node_id: ds_28_system_trait label: DS-28 system node_type: TRAIT grounding: traitmech:000452 description: Possession of a genome-encoded DS-28 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_28_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The DS-28/ANEX locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays. 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. describe the plasmid-based phage challenge used to validate predicted transcriptional units. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family\ \ nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\t\ True\tTrue\tPredicted novel defense gene\tDS-28" notes: The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t\ 24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\tDS-28\tTrue" notes: The final Science supplementary Table S8 maps ANEX to replicated display name DS-28. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN\ \ pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription\ \ termination, anti-termination, RNAP clamp, phage, transcription initiation,\ \ P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t\ 143.0\t178.0\t0.326\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-28__DS-28A | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-28__DS-28B | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: ds_28_system_trait description: DS-28-mediated phage plaquing reduction realizes the DS-28 system trait. evidence: - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\t\ True\tDefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family\ \ nuclease\tWP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\t\ True\tTrue\tPredicted novel defense gene\tDS-28" notes: The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t\ 24-07-24\t24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\ \t\tTrue\tLB\t37" notes: The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602. - 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: The DS nomenclature is used for DefensePredictor discovered systems. - subject: ds_28_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: DS-28 system possession is a phage-defense-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 validated TUs as DefensePredictor discovered systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-28 | 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-28 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science. discussions: - discussion_id: ds-28-defensefinder-model-gap prompt: Resolve DS-28 native host breadth, exact component activities, profile-to-protein mappings, HEPN and transcription-factor HHpred-domain interpretations, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-28 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: DeWeirdt et al. support DS-28 as the defensive ANEX transcriptional unit and final Science Tables S6/S7/S8 map it to product accessions WP_000494510.1 and WP_000528930.1, a Bas60 phage readout, display name DS-28, a high-probability HEPN HHpred row, and a lower-probability TF HHpred row. The pinned DefenseFinder HMM inventory records two DS-28 custom profile rows. The pinned rules table has no DS-28 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN or transcription-factor activity, molecular output, or endogenous DS-28 activity. 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 validated TUs as DSs. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx snippet: "ANEX\tNZ_RRWS01000106.1\tGCF_003892555.1\t+\tTrue\tFalse\tFalse\tTrue\t\ DefensePredictor hits\t2434\t3695\thypothetical protein, HEPN family nuclease\t\ WP_000494510.1, WP_000528930.1\t7.693635438050782\t1.093286044385436\tTrue\t\ True\tPredicted novel defense gene\tDS-28" notes: The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx snippet: "Bas60\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t400000\tANEX\t24-07-24\t\ 24-07-24_ANEX_NADH_APE1_NLRH.png\t1\t1\t\t10\t4.6020599913279625\t\t\tTrue\t\ LB\t37" notes: The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\tDS-28\tTrue" notes: The final Science supplementary Table S8 maps ANEX to replicated display name DS-28. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t1.0\t163.0\tWP_000528930.1\tHEPN\tPF18736.6\tpEK499_p136 ; HEPN\ \ pEK499 p136\thhpred_5242066.hhr\t1.0\t153.0\t1.0\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX. - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx snippet: "ANEX\t2.0\t252.0\tWP_000494510.1\tTF\t6J9E_J\tRNA polymerase, transcription\ \ termination, anti-termination, RNAP clamp, phage, transcription initiation,\ \ P7, NusA, Xanthomonos oryzae, Xp10, transcription\thhpred_1617000.hhr\t143.0\t\ 178.0\t0.326\t2024-07-30 00:00:00" notes: The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DS-28 | 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-28 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-28__DS-28A | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DS-28__DS-28B | | DS-28 | Custom | 100 |' notes: The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list DS-28, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#ds_28_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T04:57:13Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DS-28 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 ANEX transcriptional-unit level because HEPN and transcription-factor HHpred-domain interpretation and rule rows remain unresolved, and proposals/metpo_traitmech_v329 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-29T04:57:14Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DS-28 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned ANEX assays in E. coli MG1655 and a DefenseFinder DS-28 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-28 activity. No paid research was used. llm_assisted: true