TraitMech

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DS-46 system

traitmech:000471 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DS-46 locus cataloged as working transcriptional unit RMRT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (3)

  • 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
    RMRT NZ_RRVG01000021.1 GCF_003886135.1 + False False True True HHblits hits 62985 63495 DUF3606 domain-containing protein, hypothetical protein WP_001406733.1, WP_000002748.1 -4.513359272522268 5.517452896464706 False True DS-46

    The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495.

DS-46 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-46 locus to reduced bacteriophage plaquing without resolving DS-46 phage-specific readouts, domain annotations, DefenseFinder model coverage, or molecular output.

NONMECHANISTIC · The graph captures DS-46 as the validated RMRT transcriptional unit with two Table S6 product accessions. It does not assert phage-specific Table S7 readouts, Table S8 display-name rows, Table S8 HHpred-domain rows, DefenseFinder article/HMM/rules rows, native host breadth, exact component activities, molecular output, complete phage breadth, or endogenous DS-46 activity.

DS-46 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-46 system.

Edge evidence

  • DS-46 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-46/RMRT locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.

    • 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. describe the plasmid-based phage challenge used to validate predicted transcriptional units.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx RMRT NZ_RRVG01000021.1 GCF_003886135.1 + False False True True HHblits hits 62985 63495 DUF3606 domain-containing protein, hypothetical protein WP_001406733.1, WP_000002748.1 -4.513359272522268 5.517452896464706 False True DS-46 The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495.
  • reduced bacteriophage plaquing confers DS-46 system METPO:2007700

    DS-46-mediated phage plaquing reduction realizes the DS-46 system trait.

    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx RMRT NZ_RRVG01000021.1 GCF_003886135.1 + False False True True HHblits hits 62985 63495 DUF3606 domain-containing protein, hypothetical protein WP_001406733.1, WP_000002748.1 -4.513359272522268 5.517452896464706 False True DS-46 The final Science supplementary Table S6 maps working_id RMRT to DS_name DS-46, marks the cloned transcriptional unit as defensive, records an HHblits-hit screen, and places two product accessions in NZ_RRVG01000021.1 positions 62985-63495.
    • 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. The DS nomenclature is used for validated phage-defense transcriptional units.
  • DS-46 system is a phage defense system rdfs:subClassOf

    DS-46 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.

Provenance

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

Parent traits (1)

Synonyms (2)

  • DS-46 EXACT_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • RMRT RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx

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-46 phage-specific readouts, display-name and domain rows, DefenseFinder model coverage, native host breadth, exact component activities, molecular output, complete phage breadth, and endogenous activity before minting narrower DS-46 mechanism children.

KNOWLEDGE GAP OPEN ds-46-model-coverage-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_46_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-46 as the defensive RMRT transcriptional unit and final Science Table S6 maps RMRT to two product accessions. A first-pass final Science Table S7/S8 review found no exact RMRT/DS-46 phage-specific readout, display-name row, or HHpred-domain row. The pinned DefenseFinder article, HMM, and rules registries also do not list DS-46 or RMRT, and the first-pass record therefore does not resolve native host breadth, complete phage breadth, exact component activities, molecular output, or endogenous DS-46 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-46 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 RMRT transcriptional-unit level because phage-specific Table S7 readouts, Table S8 display and domain rows, DefenseFinder article/HMM/rules coverage, native host breadth, exact component activities, complete phage breadth, and molecular output remain unresolved, and proposals/metpo_traitmech_v348 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-46 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RMRT assays in E. coli MG1655, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-46 activity. No paid research was used.