TraitMech

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DS-11 system

traitmech:000435 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 11 locus cataloged as working transcriptional unit IMPD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (10)

  • 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 validated 42 predicted transcriptional units as phage-defense systems in E. coli.

  • 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 validated transcriptional units as DefensePredictor discovered systems.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
    IMPD NZ_RRVY01000003.1 GCF_003886375.1 + True False False True DefensePredictor hits 365785 366882 CBS domain-containing protein WP_000257686.1 4.37610109478113 1.840433765255303 True True Predicted novel defense gene DS-11

    The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    T3 1.1 pLAND 24-03-08_NYND_PIN2_MHAD_EV.png 300000000 IMPD 24-03-08 24-03-08_MNAC_GHOS_BRNT_IMPD.png 5 3 300000 3 True LB 37

    The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    T3 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 200000000 IMPD 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 5 4 400000 2.698970004 Bas67 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 IMPD 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 5 5 500000 1.602059991 T3 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 200000000 IMPD Y157A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 8 2 200000000 0 Bas67 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 IMPD Y157A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 7 2 20000000 0 T3 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 200000000 IMPD R330A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 8 3 300000000 -0.1760912591 Bas67 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 IMPD R330A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 7 3 30000000 -0.1760912591 T3 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 200000000 IMPD H335A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 8 1 100000000 0.3010299957 Bas67 B.2 MG1655 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 IMPD H335A 24-07-18 24-07-18_IMPD-Y157A_IMPD_IMPD-R330A_IMPD-H335A_HIPA_HIPA-D139A.png 6 6 6000000 0.5228787453

    The final Science supplementary Table S7 System Mutants sheet pairs wild-type IMPD with IMPD Y157A, R330A, and H335A rows in T3 and Bas67 assay panels.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    IMPD DS-11 True

    The final Science supplementary Table S8 maps IMPD to replicated display name DS-11.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    IMPD 1.0 365.0 WP_000257686.1 HEPN PF18731.5 HEPN_Swt1 ; Swt1-like HEPN hhpred_1021051.hhr 252.0 359.0 0.98 2024-04-16 00:00:00

    The final Science supplementary Table S8 reports a HEPN HHpred hit for WP_000257686.1 in IMPD.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    IMPD 1.0 365.0 WP_000257686.1 CBS cd04614 CBS_pair_arch2_repeat2; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea hhpred_1021051.hhr 134.0 241.0 0.9916 2024-04-16 00:00:00

    The final Science supplementary Table S8 reports a CBS HHpred hit for WP_000257686.1 in IMPD.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | DS-11 | 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-11 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | DS-11__DS-11 | | DS-11 | Custom | 100 |

    The pinned DefenseFinder HMM inventory records DS-11__DS-11 as a custom DS-11 profile.

DS-11 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-11 locus to reduced bacteriophage plaquing without resolving DS-11 component function or effector activity.

NONMECHANISTIC · The graph captures DS-11 as the validated IMPD transcriptional unit with one product accession, final Table S8 HEPN and CBS HHpred-domain rows, and one DefenseFinder DS-11 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or ligand, the HEPN substrate, whether ATP binding or CBS-ligand binding activates the effector, phage target breadth, or DefenseFinder rule-level detection criteria.

DS-11 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-11 system.

Edge evidence

  • DS-11 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-11/IMPD locus contributes to reduced bacteriophage plaquing when plasmid expressed.

  • reduced bacteriophage plaquing confers DS-11 system METPO:2007700

    DS-11-mediated phage plaquing reduction realizes the DS-11 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 IMPD NZ_RRVY01000003.1 GCF_003886375.1 + True False False True DefensePredictor hits 365785 366882 CBS domain-containing protein WP_000257686.1 4.37610109478113 1.840433765255303 True True Predicted novel defense gene DS-11 The final Science supplementary Table S6 maps working_id IMPD to DS_name DS-11, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000003.1 positions 365785-366882 with product accession WP_000257686.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx T3 1.1 pLAND 24-03-08_NYND_PIN2_MHAD_EV.png 300000000 IMPD 24-03-08 24-03-08_MNAC_GHOS_BRNT_IMPD.png 5 3 300000 3 True LB 37 The final Science supplementary Table S7 reports an IMPD assay row with a T3 phage readout and a -log(EOP) value of 3.0.
  • DS-11 system is a phage defense system rdfs:subClassOf

    DS-11 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-11 | 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-11 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-11 EXACT_SYNONYM · DOI:10.1126/science.adv7924
  • IMPD RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • DS-11__DS-11 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-11 native host breadth, profile-to-protein mapping, sensitive-phage breadth, direct viral trigger, direct HEPN-family nuclease substrate, CBS-ligand or ATP-dependent activation model, and rule-level detection criteria before minting narrower DS-11 mechanism children.

KNOWLEDGE GAP OPEN ds-11-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_11_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-11 as the defensive IMPD transcriptional unit that reduced T3 and Bas67 plaquing when cloned in E. coli MG1655, and the final Table S8 HHpred sheet reports HEPN and CBS hits for the single IMPD product. The pinned DefenseFinder HMM inventory records one DS-11 profile row, the pinned rules table has no DS-11 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, the direct HEPN substrate, the activation ligand, phage target breadth, or endogenous DS-11 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-11 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 IMPD transcriptional-unit level because HEPN/CBS domain and mutant readouts do not resolve native DS-11 activation or effector chemistry and proposals/metpo_traitmech_v312 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-11 system canonical_examples and left them empty because DeWeirdt et al. support cloned IMPD plaquing assays in E. coli MG1655 plus a DefenseFinder DS-11 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-11 activity. No paid research was used.

  3. · ADDRESSED_PR_REVIEW · codex

    Resolved PR #1403 review issue #1404 by broadening the DS-11 reduced-phage-plaquing node description so it no longer names only T3 while the evidence bundle includes Bas67 rows.