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DS-7 system

traitmech:000431 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 7 locus cataloged with working_id SVIR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (11)

DS-7 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-7 locus to reduced bacteriophage plaquing without resolving DS-7 component function or effector activity.

NONMECHANISTIC · The graph captures DS-7 as the validated SVIR transcriptional unit with one product accession and with a DefenseFinder DS-7 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, the exact HNH endonuclease activity, phage-baseplate-like domain relevance, phage target breadth, or DefenseFinder rule-level detection criteria.

DS-7 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-7 system.

Edge evidence

  • DS-7 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-7/SVIR locus contributes to reduced bacteriophage plaquing when plasmid expressed.

    • DOI:10.1126/science.adv7924 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 DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx SVIR NZ_QOYF01000007.1 GCF_003334585.1 + True False False True DefensePredictor hits 310084 311190 DUF2634 domain-containing protein WP_225403053.1 5.785481186679323 3.623314765621056 True True Predicted novel defense gene DS-7 The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 5000000 SVIR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 2 100 10000 2.6989700043360187 True LB 37 The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 A.1 MG1655 24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png 3000000 SVIR 24-07-12 24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png 4 14 140000 1.330993219 Bas60 A.1 MG1655 24-07-10_EV_MNAC-K375A_MNAC-N84A_MNAC-D52A.png 3000000 SVIR H52A 24-07-12 24-07-12_HIPA_HIPA-D139A_SVIR_SVIR-H52A_DISA_DISA-D433A.png 5 10 1000000 0.4771212547 The final Science supplementary Table S7 System Mutants sheet pairs wild-type SVIR and SVIR H52A in a Bas60 assay panel, with -log(EOP) shifting from 1.331 to 0.477 for the H52A mutant.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 B.1 MG1655 24-07-17_MVB1_VPUS_VAME_EV.png 400000 SVIR 24-07-18 24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png 0 1 1 5.602059991 Bas60 B.1 MG1655 24-07-17_MVB1_VPUS_VAME_EV.png 400000 SVIR H52A 24-07-18 24-07-18_DISA-R468A_DISA_SVIR_DISA-D433A_SVIR-H52A.png 4 22 220000 0.2596373105 The final Science supplementary Table S7 System Mutants sheet records a second SVIR versus SVIR H52A Bas60 panel, with -log(EOP) shifting from 5.602 to 0.260 for the H52A mutant.
  • reduced bacteriophage plaquing confers DS-7 system METPO:2007700

    DS-7-mediated phage plaquing reduction realizes the DS-7 system trait.

    • DOI:10.1126/science.adv7924 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. DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx SVIR NZ_QOYF01000007.1 GCF_003334585.1 + True False False True DefensePredictor hits 310084 311190 DUF2634 domain-containing protein WP_225403053.1 5.785481186679323 3.623314765621056 True True Predicted novel defense gene DS-7 The final Science supplementary Table S6 maps working_id SVIR to DS_name DS-7, marks the cloned transcriptional unit as defensive, and records NZ_QOYF01000007.1 positions 310084-311190 with product accession WP_225403053.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 5000000 SVIR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 2 100 10000 2.6989700043360187 True LB 37 The final Science supplementary Table S7 reports an SVIR assay row with a Bas60 phage readout and a -log(EOP) value of 2.699.
  • DS-7 system is a phage defense system rdfs:subClassOf

    DS-7 system possession is a phage-defense-system trait.

    • DOI:10.1126/science.adv7924 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 DeWeirdt et al. validate DSs as anti-phage systems.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-7 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | The pinned DefenseFinder article registry maps the DS-7 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1126/science.adv7924

Parent traits (1)

Synonyms (3)

  • DS-7 EXACT_SYNONYM · DOI:10.1126/science.adv7924
  • SVIR RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • DS-7__DS-7 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve DS-7 native host breadth, exact single-component activity, DS-7 profile-to-protein mapping, sensitive-phage breadth, HNH endonuclease activity, the role of the H52 residue, the phage-baseplate-like hit, and rule-level detection criteria before minting narrower DS-7 mechanism children.

KNOWLEDGE GAP OPEN ds-7-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_7_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-7 as the defensive SVIR transcriptional unit that reduced Bas60 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records one DS-7 profile row. The pinned rules table has no DS-7 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, HNH endonuclease activity, the function of the H52 residue, phage target breadth, or endogenous DS-7 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-7 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 SVIR transcriptional-unit level because the pinned DefenseFinder DS-7 HMM row is not backed by a rules row; proposals/metpo_traitmech_v308 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-7 system canonical_examples and left them empty because DeWeirdt et al. support cloned SVIR plaquing assays in E. coli MG1655 plus a DefenseFinder DS-7 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-7 activity. No paid research was used.