identifier: traitmech:000447
label: DS-22 system
definition: A phage defense system in which an organism possesses the single-gene
  DefensePredictor-discovered system 22 locus cataloged as working transcriptional
  unit MVB1 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-22
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: MVB1
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-22__DS-22
  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: "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\t\
    DefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t9.664065793183475\t\
    -2.806015014798907\tTrue\tFalse\tPredicted novel defense gene\tDS-22"
  notes: The final Science supplementary Table S6 maps working_id MVB1 to DS_name
    DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1
    positions 10119-11351 with product accession WP_000162952.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t24-07-17\t\
    24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37"
  notes: The final Science supplementary Table S7 reports an MVB1 assay row with a
    Bas11 phage readout and a -log(EOP) value of 5.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "MVB1\tDS-22\tTrue"
  notes: The final Science supplementary Table S8 maps MVB1 to replicated display
    name DS-22.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "MVB1\t1.0\t410.0\tWP_000162952.1\tMvb12\tPF09452.15\tMvb12 ; ESCRT-I subunit\
    \ Mvb12\thhpred_4626820.hhr\t33.0\t64.0\t0.72\t2024-07-27 00:00:00\t\t"
  notes: The final Science supplementary Table S8 reports a low-probability Mvb12
    HHpred hit for WP_000162952.1 in MVB1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "MVB1\t1.0\t410.0\tWP_000162952.1\tJAB\tPF04002.20\tRadC-like JAB domain\t\
    hhpred_4626820.hhr\t258.0\t324.0\t0.37\t2024-07-27 00:00:00\t\t"
  notes: The final Science supplementary Table S8 reports a low-probability JAB HHpred
    hit for WP_000162952.1 in MVB1.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-22 | 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-22 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-22__DS-22                                     |                                                  |
    DS-22                  | Custom                  | 60     |'
  notes: The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22
    profile.
causal_graphs:
- graph_id: ds_22_locus_reduces_phage_plaquing
  title: DS-22 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the single-gene DS-22 locus
    to reduced bacteriophage plaquing without resolving DS-22 component function or
    molecular output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-22 as the validated MVB1 transcriptional unit
    with one product accession and one DefenseFinder DS-22 profile row. It does not
    assert native host breadth, exact profile-to-protein correspondence, DS-22 molecular
    activity, trigger, substrate, low-confidence HHpred-domain interpretations, complete
    phage breadth, or DefenseFinder rule-level detection criteria.
  nodes:
  - node_id: ds_22_locus
    label: DS-22 locus
    node_type: GENETIC_ELEMENT
    description: A single-gene DefensePredictor-discovered system 22 locus represented
      in the pinned DefenseFinder HMM inventory by one DS-22 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced efficiency of plaquing by bacteriophage Bas11 in cells carrying
      cloned MVB1.
  - node_id: ds_22_system_trait
    label: DS-22 system
    node_type: TRAIT
    grounding: traitmech:000447
    description: Possession of a genome-encoded DS-22 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_22_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-22/MVB1 locus contributes to reduced bacteriophage plaquing
      when plasmid expressed.
    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 validate DefensePredictor-discovered systems
        by assaying cloned transcriptional units against E. coli phages.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t\
        9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense\
        \ gene\tDS-22"
      notes: The final Science supplementary Table S6 maps working_id MVB1 to DS_name
        DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1
        positions 10119-11351 with product accession WP_000162952.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t\
        24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t\
        37"
      notes: The final Science supplementary Table S7 reports an MVB1 assay row with
        a Bas11 phage readout and a -log(EOP) value of 5.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "MVB1\tDS-22\tTrue"
      notes: The final Science supplementary Table S8 maps MVB1 to replicated display
        name DS-22.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-22__DS-22                                     |                                                  |
        DS-22                  | Custom                  | 60     |'
      notes: The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom
        DS-22 profile.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_22_system_trait
    description: DS-22-mediated phage plaquing reduction realizes the DS-22 system
      trait.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t\
        9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense\
        \ gene\tDS-22"
      notes: The final Science supplementary Table S6 maps working_id MVB1 to DS_name
        DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1
        positions 10119-11351 with product accession WP_000162952.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t\
        24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t\
        37"
      notes: The final Science supplementary Table S7 reports an MVB1 assay row with
        a Bas11 phage readout and a -log(EOP) value of 5.
    - 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_22_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-22 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-22 | 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-22 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-22-defensefinder-model-gap
  prompt: Resolve DS-22 native host breadth, exact single-component activity, profile-to-protein
    mapping, sensitive-phage breadth, low-confidence HHpred-domain interpretation,
    molecular output, and rule-level DefenseFinder criteria before minting narrower
    DS-22 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-22 as the defensive MVB1 transcriptional unit
    that reduced Bas11 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder
    HMM inventory records one DS-22 profile row. The pinned rules table has no DS-22
    row, and the first-pass record does not resolve native host breadth, exact component
    activity, direct profile-to-protein correspondence, the Mvb12 and JAB HHpred-domain
    rows, phage target breadth, molecular output, or endogenous DS-22 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: "MVB1\tNZ_QOWO01000045.1\tGCF_003334815.1\t-\tTrue\tFalse\tFalse\tTrue\t\
      DefensePredictor hits\t10119\t11351\thypothetical protein\tWP_000162952.1\t\
      9.664065793183475\t-2.806015014798907\tTrue\tFalse\tPredicted novel defense\
      \ gene\tDS-22"
    notes: The final Science supplementary Table S6 maps working_id MVB1 to DS_name
      DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1
      positions 10119-11351 with product accession WP_000162952.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas11\t6.1\tpLAND\t24-07-17_MVB1_VPUS_VAME_EV.png\t100000000\tMVB1\t\
      24-07-17\t24-07-17_MVB1_VPUS_VAME_EV.png\t2\t10\t\t1000\t5\t\t\tTrue\tLB\t37"
    notes: The final Science supplementary Table S7 reports an MVB1 assay row with
      a Bas11 phage readout and a -log(EOP) value of 5.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "MVB1\tDS-22\tTrue"
    notes: The final Science supplementary Table S8 maps MVB1 to replicated display
      name DS-22.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "MVB1\t1.0\t410.0\tWP_000162952.1\tMvb12\tPF09452.15\tMvb12 ; ESCRT-I\
      \ subunit Mvb12\thhpred_4626820.hhr\t33.0\t64.0\t0.72\t2024-07-27 00:00:00\t\
      \t"
    notes: The final Science supplementary Table S8 reports a low-probability Mvb12
      HHpred hit for WP_000162952.1 in MVB1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "MVB1\t1.0\t410.0\tWP_000162952.1\tJAB\tPF04002.20\tRadC-like JAB domain\t\
      hhpred_4626820.hhr\t258.0\t324.0\t0.37\t2024-07-27 00:00:00\t\t"
    notes: The final Science supplementary Table S8 reports a low-probability JAB
      HHpred hit for WP_000162952.1 in MVB1.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-22 | 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-22 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-22__DS-22                                     |                                                  |
      DS-22                  | Custom                  | 60     |'
    notes: The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom
      DS-22 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-22, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_22_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-28'
curation_history:
- timestamp: '2026-09-28T23:30:13Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-22 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 MVB1 transcriptional-unit
    level because the pinned DefenseFinder DS-22 HMM row is not backed by a rules
    row, and proposals/metpo_traitmech_v324 reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-28T23:30:14Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-22 system canonical_examples and left them empty because DeWeirdt
    et al. directly support cloned MVB1 assays in E. coli MG1655 and a DefenseFinder
    DS-22 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-22 activity. No paid research was used.
  llm_assisted: true
- timestamp: '2026-09-29T00:00:35Z'
  curator: codex
  action: UPDATED_EVIDENCE
  changes: Added exact final Table S8 MVB1 HHpred-domain rows for the low-probability
    Mvb12 and JAB hits so the DS-22 mechanism gap quotes the evidence it defers.
  llm_assisted: true
- timestamp: '2026-09-29T00:11:21Z'
  curator: codex
  action: UPDATED_SYNONYM_SOURCE
  changes: Aligned the DS-22 exact-synonym source with adjacent DS system records
    by citing the DOI that defines the DS display-name convention.
  llm_assisted: true
- timestamp: '2026-09-29T00:23:32Z'
  curator: codex
  action: UPDATED_EVIDENCE
  changes: Split the MVB1 Mvb12 and JAB Table S8 HHpred rows into separate evidence
    items so each snippet quotes one contiguous source row.
  llm_assisted: true