TraitMech

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DS-12 system

traitmech:000436 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 12 locus cataloged as working transcriptional unit PD3A and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (10)

DS-12 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-12 locus to reduced bacteriophage plaquing without resolving DS-12 component function or effector activity.

NONMECHANISTIC · The graph captures DS-12 as the validated PD3A transcriptional unit with two product accessions, final Table S8 ABC ATPase, PDDEXK, and NACHT HHpred-domain rows, and one DefenseFinder DS-12B profile row. It does not assert native host breadth, DS-12A model coverage, exact DS-12B profile-to-protein correspondence, the direct viral trigger or substrate, exact ABC ATPase or nuclease chemistry, phage target breadth, or DefenseFinder rule-level detection criteria.

DS-12 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-12 system.

Edge evidence

  • DS-12 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-12/PD3A locus contributes to reduced bacteriophage plaquing when plasmid expressed.

  • reduced bacteriophage plaquing confers DS-12 system METPO:2007700

    DS-12-mediated phage plaquing reduction realizes the DS-12 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 PD3A NZ_RRVF01000002.1 GCF_003886115.1 - True False True True DefensePredictor hits 104144 108678 restriction endonuclease, AAA family ATPase WP_059339975.1, WP_064766070.1 14.31811904122612 6.906754778648663 True True Remote defense homolog DS-12 The final Science supplementary Table S6 maps working_id PD3A to DS_name DS-12, marks the cloned transcriptional unit as defensive, and records NZ_RRVF01000002.1 positions 104144-108678 with product accessions WP_059339975.1 and WP_064766070.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas25 4.2 pLAND 24-05-17_EV_HHNH.png 200000000 PD3A 24-05-17 24-05-17_VAME_AAA1_PD3A_PDP7.png 3 2 2000 5 True LB 37 The final Science supplementary Table S7 reports a PD3A assay row with a Bas25 phage readout and a -log(EOP) value of 5.0.
  • DS-12 system is a phage defense system rdfs:subClassOf

    DS-12 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-12B | 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-12B 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-12 EXACT_SYNONYM · DOI:10.1126/science.adv7924
  • PD3A RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • DS-12__DS-12B 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-12 native host breadth, DS-12A model coverage, DS-12B profile-to-protein mapping, sensitive-phage breadth, direct viral trigger or substrate, exact ABC ATPase and PDDEXK/nSTAND nuclease chemistry, and rule-level detection criteria before minting narrower DS-12 mechanism children.

KNOWLEDGE GAP OPEN ds-12-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_12_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-12 as the defensive PD3A transcriptional unit that reduced Bas25 plaquing when cloned in E. coli MG1655, and the final Table S8 HHpred sheet reports ABC ATPase, PDDEXK, and NACHT hits across the two PD3A products. The pinned DefenseFinder HMM inventory records one DS-12B profile row, the pinned article registry names DS-12B rather than DS-12, the pinned rules table has no DS-12 row, and the first-pass record does not resolve native host breadth, DS-12A model coverage, exact profile-to-protein correspondence, direct ATPase or nuclease activity, phage target breadth, or endogenous DS-12 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-12 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 PD3A transcriptional-unit level because the pinned DefenseFinder DS-12B HMM row leaves DS-12A coverage unresolved and proposals/metpo_traitmech_v313 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-12 system canonical_examples and left them empty because DeWeirdt et al. support cloned PD3A plaquing assays in E. coli MG1655 plus a partial DefenseFinder DS-12B model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-12 activity. No paid research was used.