identifier: traitmech:000454
label: DS-31 system
definition: A phage defense system in which an organism possesses the single-gene
  DefensePredictor-discovered system 31 locus cataloged as working transcriptional
  unit RED7 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.
definition_source: DOI:10.1126/science.adv7924
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: DS-31
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: RED7
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-31__DS-31
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1126/science.adv7924
  snippet: 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
  notes: DeWeirdt et al. experimentally validated 42 predicted transcriptional units
    as phage-defense systems in E. coli.
- reference: DOI:10.1126/science.adv7924
  snippet: 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.
  notes: DeWeirdt et al. name validated transcriptional units as DefensePredictor
    discovered systems.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  snippet: "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\t\
    DefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t\
    1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31"
  notes: The final Science supplementary Table S6 maps working_id RED7 to DS_name
    DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1
    positions 6615-7667 with product accession WP_001703029.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t\
    24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\
    37"
  notes: The final Science supplementary Table S7 reports a RED7 assay row with a
    Bas19 phage readout and a -log(EOP) value of 6.342.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "RED7\tDS-31\tTrue"
  notes: The final Science supplementary Table S8 maps RED7 to replicated display
    name DS-31.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination\
    \ protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t201-203\t\
    187.0"
  notes: The final Science supplementary Table S8 reports a high-probability PDDEXK
    HHpred hit for WP_001703029.1 in RED7.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-31 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
    learning model to discover novel prokaryotic immune systems | '
  notes: The pinned DefenseFinder article registry maps the DS-31 source key to the
    preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been
    published in Science.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| DS-31__DS-31                                     |                                                  |
    DS-31                  | Custom                  | 170    |'
  notes: The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31
    profile.
causal_graphs:
- graph_id: ds_31_locus_reduces_phage_plaquing
  title: DS-31 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the single-gene DS-31 locus
    to reduced bacteriophage plaquing without resolving DS-31 component function or
    molecular output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-31 as the validated RED7 transcriptional unit
    with one product accession, one high-probability PDDEXK HHpred-domain row, and
    one DefenseFinder DS-31 profile row. It does not assert native host breadth, exact
    profile-to-protein correspondence, DS-31 molecular activity, trigger, substrate,
    complete phage breadth, PDDEXK HHpred-domain interpretation, or DefenseFinder
    rule-level detection criteria.
  nodes:
  - node_id: ds_31_locus
    label: DS-31 locus
    node_type: GENETIC_ELEMENT
    description: A single-gene DefensePredictor-discovered system 31 locus represented
      in the pinned DefenseFinder HMM inventory by one DS-31 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced bacteriophage plaquing in cells carrying cloned RED7.
  - node_id: ds_31_system_trait
    label: DS-31 system
    node_type: TRAIT
    grounding: traitmech:000454
    description: Possession of a genome-encoded DS-31 phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: ds_31_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-31/RED7 locus contributes to reduced bacteriophage plaquing
      in heterologous E. coli MG1655 plasmid-expression assays.
    evidence:
    - reference: DOI:10.1126/science.adv7924
      snippet: 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
      notes: DeWeirdt et al. describe the plasmid-based phage challenge used to validate
        predicted transcriptional units.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t\
        8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\t\
        DS-31"
      notes: The final Science supplementary Table S6 maps working_id RED7 to DS_name
        DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1
        positions 6615-7667 with product accession WP_001703029.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t\
        24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\
        \t\tTrue\tLB\t37"
      notes: The final Science supplementary Table S7 reports a RED7 assay row with
        a Bas19 phage readout and a -log(EOP) value of 6.342.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "RED7\tDS-31\tTrue"
      notes: The final Science supplementary Table S8 maps RED7 to replicated display
        name DS-31.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination\
        \ protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t\
        201-203\t187.0"
      notes: The final Science supplementary Table S8 reports a high-probability PDDEXK
        HHpred hit for WP_001703029.1 in RED7.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-31__DS-31                                     |                                                  |
        DS-31                  | Custom                  | 170    |'
      notes: The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom
        DS-31 profile.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_31_system_trait
    description: DS-31-mediated phage plaquing reduction realizes the DS-31 system
      trait.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t\
        8.059866321466373\t1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\t\
        DS-31"
      notes: The final Science supplementary Table S6 maps working_id RED7 to DS_name
        DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1
        positions 6615-7667 with product accession WP_001703029.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t\
        24-07-25\t24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\
        \t\tTrue\tLB\t37"
      notes: The final Science supplementary Table S7 reports a RED7 assay row with
        a Bas19 phage readout and a -log(EOP) value of 6.342.
    - reference: DOI:10.1126/science.adv7924
      snippet: 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.
      notes: The DS nomenclature is used for DefensePredictor discovered systems.
  - subject: ds_31_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-31 system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1126/science.adv7924
      snippet: 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.
      notes: DeWeirdt et al. name validated TUs as DefensePredictor discovered systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| DS-31 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
        learning model to discover novel prokaryotic immune systems | '
      notes: The pinned DefenseFinder article registry maps the DS-31 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-31-defensefinder-model-gap
  prompt: Resolve DS-31 native host breadth, exact single-component activity, profile-to-protein
    mapping, PDDEXK HHpred-domain interpretation, complete phage breadth, molecular
    output, and rule-level DefenseFinder criteria before minting narrower DS-31 mechanism
    children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-31 as the defensive RED7 transcriptional unit
    and final Science Tables S6/S7/S8 map it to product accession WP_001703029.1,
    a Bas19 phage readout, display name DS-31, and a PDDEXK HHpred row. The pinned
    DefenseFinder HMM inventory records one DS-31 custom profile row. The pinned rules
    table has no DS-31 row, and the first-pass record does not resolve native host
    breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK
    activity, molecular output, or endogenous DS-31 activity.
  evidence:
  - reference: DOI:10.1126/science.adv7924
    snippet: 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.
    notes: DeWeirdt et al. name validated TUs as DSs.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
    snippet: "RED7\tNZ_QOWW01000064.1\tGCF_003334245.1\t-\tTrue\tFalse\tFalse\tTrue\t\
      DefensePredictor hits\t6615\t7667\thypothetical protein\tWP_001703029.1\t8.059866321466373\t\
      1.02528101558256\tTrue\tTrue\tPredicted novel defense gene\tDS-31"
    notes: The final Science supplementary Table S6 maps working_id RED7 to DS_name
      DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1
      positions 6615-7667 with product accession WP_001703029.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas19\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t2200000\tRED7\t24-07-25\t\
      24-07-25_PDP1_RED1_PDP4_RED7.png\t0\t1\t\t1\t6.342422680822207\t\t\tTrue\tLB\t\
      37"
    notes: The final Science supplementary Table S7 reports a RED7 assay row with
      a Bas19 phage readout and a -log(EOP) value of 6.342.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "RED7\tDS-31\tTrue"
    notes: The final Science supplementary Table S8 maps RED7 to replicated display
      name DS-31.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "RED7\t1.0\t350.0\tWP_001703029.1\tPDDEXK\tPF03838.19\tRecU ; Recombination\
      \ protein U\thhpred_7098417.hhr\t56.0\t182.0\t0.99\t2024-07-28 00:00:00\t201-203\t\
      187.0"
    notes: The final Science supplementary Table S8 reports a high-probability PDDEXK
      HHpred hit for WP_001703029.1 in RED7.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-31 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine
      learning model to discover novel prokaryotic immune systems | '
    notes: The pinned DefenseFinder article registry maps the DS-31 source key to
      the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since
      been published in Science.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| DS-31__DS-31                                     |                                                  |
      DS-31                  | Custom                  | 170    |'
    notes: The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom
      DS-31 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-31, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_31_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-29'
curation_history:
- timestamp: '2026-09-29T06:35:29Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-31 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 RED7 transcriptional-unit
    level because PDDEXK activity and rule rows remain unresolved, and proposals/metpo_traitmech_v331
    reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-29T06:35:30Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-31 system canonical_examples and left them empty because DeWeirdt
    et al. directly support cloned RED7 assays in E. coli MG1655 and a DefenseFinder
    DS-31 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-31 activity. No paid research was used.
  llm_assisted: true