TraitMech

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DS-26 system

traitmech:000472 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 26 locus cataloged as working transcriptional unit NERD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (7)

  • 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
    NERD NZ_QOXL01000006.1 GCF_003334035.1 - True False False True DefensePredictor hits 203139 204737 hypothetical protein WP_054626965.1 9.096479385650875 4.498799058824351 True True Remote defense homolog DS-26

    The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    Bas25 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 50000000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 6.221848749616356 True LB 37

    The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 2 20 5.041392685158225 True LB 37

    The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    NERD DS-26 True

    The final Science supplementary Table S8 maps NERD to replicated display name DS-26.

  • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    NERD 1.0 532.0 WP_054626965.1 PDDEXK PF09254.16 FokI_cleav_dom ; FokI, cleavage domain hhpred_1843394.hhr 282.0 459.0 0.95 2024-07-29 00:00:00 77-79 63.0

    The final Science supplementary Table S8 reports a PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1 in NERD; this first-pass record records it as source context without resolving DS-26 molecular activity.

DS-26 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-26 locus to reduced bacteriophage plaquing without resolving DS-26 nuclease chemistry, native activity, DefenseFinder model coverage, or molecular output.

NONMECHANISTIC · The graph captures DS-26 as the validated NERD transcriptional unit with one product accession, two Table S7 phage-specific readouts, and one Table S8 PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1. It does not assert exact domain interpretation, nuclease chemistry, native host breadth, complete phage breadth, DefenseFinder article/HMM/rules coverage, molecular output, or endogenous DS-26 activity.

DS-26 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-26 system.

Edge evidence

  • DS-26 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-26/NERD 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 NERD NZ_QOXL01000006.1 GCF_003334035.1 - True False False True DefensePredictor hits 203139 204737 hypothetical protein WP_054626965.1 9.096479385650875 4.498799058824351 True True Remote defense homolog DS-26 The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas25 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 50000000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 6.221848749616356 True LB 37 The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 2 20 5.041392685158225 True LB 37 The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NERD DS-26 True The final Science supplementary Table S8 maps NERD to replicated display name DS-26.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NERD 1.0 532.0 WP_054626965.1 PDDEXK PF09254.16 FokI_cleav_dom ; FokI, cleavage domain hhpred_1843394.hhr 282.0 459.0 0.95 2024-07-29 00:00:00 77-79 63.0 The final Science supplementary Table S8 reports a PDDEXK/FokI cleavage-domain HHpred lead for WP_054626965.1 in NERD; this first-pass record records it as source context without resolving DS-26 molecular activity.
  • reduced bacteriophage plaquing confers DS-26 system METPO:2007700

    DS-26-mediated phage plaquing reduction realizes the DS-26 system trait.

    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx NERD NZ_QOXL01000006.1 GCF_003334035.1 - True False False True DefensePredictor hits 203139 204737 hypothetical protein WP_054626965.1 9.096479385650875 4.498799058824351 True True Remote defense homolog DS-26 The final Science supplementary Table S6 maps working_id NERD to DS_name DS-26, marks the cloned transcriptional unit as defensive, and records NZ_QOXL01000006.1 positions 203139-204737 with product accession WP_054626965.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas25 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 50000000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 6.221848749616356 True LB 37 The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas25 phage readout and a -log(EOP) value of 6.222.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 NERD 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 2 20 5.041392685158225 True LB 37 The final Science supplementary Table S7 Systems sheet reports a NERD assay row with a Bas19 phage readout and a -log(EOP) value of 5.041.
    • 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 DefensePredictor discovered systems.
  • DS-26 system is a phage defense system rdfs:subClassOf

    DS-26 system possession is a phage-defense-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 validated TUs as DSs.

Provenance

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

Parent traits (1)

Synonyms (2)

  • DS-26 EXACT_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • NERD 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-26 native host breadth, exact component activity, PDDEXK/FokI HHpred-domain interpretation, nuclease chemistry, complete phage breadth, molecular output, and DefenseFinder model coverage before minting narrower DS-26 mechanism children.

KNOWLEDGE GAP OPEN ds-26-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_26_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-26 as the defensive NERD transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas25 and Bas19 phage readouts, display name DS-26, and a PDDEXK/FokI cleavage-domain HHpred row. A first-pass pinned DefenseFinder review found no exact DS-26 article, HMM, or rules row, and the first-pass record therefore does not resolve native host breadth, complete phage breadth, domain interpretation, nuclease chemistry, molecular output, or endogenous DS-26 activity.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-26 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 NERD transcriptional-unit level because native host breadth, exact component activity, complete phage breadth, DefenseFinder model coverage, nuclease chemistry, and molecular output remain unresolved, and proposals/metpo_traitmech_v349 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-26 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned NERD assays in E. coli MG1655, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-26 activity. No paid research was used.