TraitMech

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DS-3 system

traitmech:000426 · CLASS · PROPOSED

A phage defense system in which an organism possesses the one-gene DefensePredictor-discovered system 3 locus cataloged as working transcriptional unit PIN8 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (9)

DS-3 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the one-gene DS-3 locus to reduced bacteriophage plaquing without resolving DS-3 effector activity.

NONMECHANISTIC · The graph captures DS-3 as the validated PIN8 transcriptional unit with one product accession and with a DefenseFinder DS-3 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.

DS-3 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-3 system.

Edge evidence

  • DS-3 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-3/PIN8 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.
    • DOI:10.1126/science.adv7924 When we mutated catalytic residues in DS-3, the system no longer defended against phage, suggesting this domain is essential for protection. DeWeirdt et al. show DS-3 protection depends on predicted catalytic residues.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx PIN8 NZ_RRWT01000005.1 GCF_003892645.1 + True False False True DefensePredictor hits 244326 245348 hypothetical protein WP_022645725.1 8.909458355458062 -2.350827761940385 True False Predicted novel defense gene DS-3 The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx RB69 1.1 pLAND 24-03-08_NYND_PIN2_MHAD_EV.png 400000 PIN8 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 5.6020599913279625 True LB 37 The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-3__DS-3 | | DS-3 | Custom | 50 | The pinned DefenseFinder HMM inventory records DS-3__DS-3 as a custom DS-3 profile.
  • reduced bacteriophage plaquing confers DS-3 system METPO:2007700

    DS-3-mediated phage plaquing reduction realizes the DS-3 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 PIN8 NZ_RRWT01000005.1 GCF_003892645.1 + True False False True DefensePredictor hits 244326 245348 hypothetical protein WP_022645725.1 8.909458355458062 -2.350827761940385 True False Predicted novel defense gene DS-3 The final Science supplementary Table S6 maps working_id PIN8 to DS_name DS-3, marks the cloned transcriptional unit as defensive, and records NZ_RRWT01000005.1 positions 244326-245348 with product accession WP_022645725.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx RB69 1.1 pLAND 24-03-08_NYND_PIN2_MHAD_EV.png 400000 PIN8 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 5.6020599913279625 True LB 37 The final Science supplementary Table S7 reports a PIN8 assay row with an RB69 readout and a -log(EOP) value of 5.602.
  • DS-3 system is a phage defense system rdfs:subClassOf

    DS-3 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-3 | 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-3 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-3 EXACT_SYNONYM · DOI:10.1126/science.adv7924
  • PIN8 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • DS-3__DS-3 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-3 native host breadth, exact PIN ribonuclease activity, DS-3 profile-to-protein mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-3 mechanism children.

KNOWLEDGE GAP OPEN ds-3-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_3_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-3 as the defensive PIN8 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records a DS-3 profile row. The pinned rules table has no DS-3 row, and the first-pass record does not resolve native host breadth, exact PIN substrate or output, profile-to-protein mapping, phage target breadth, or endogenous DS-3 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-3 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 PIN8 transcriptional-unit level because the pinned DefenseFinder DS-3 HMM row is not backed by a rules row; proposals/metpo_traitmech_v303 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-3 system canonical_examples and left them empty because DeWeirdt et al. support cloned PIN8 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-3 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-3 activity. No paid research was used.