identifier: traitmech:000439
label: DS-16 system
definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered
  system 16 locus cataloged as working transcriptional unit PLIK 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-16
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: PLIK
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-16__DS-16A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: DS-16__DS-16B
  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: "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\t\
    DefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing\
    \ protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\t\
    True\tTrue\tStructural defense homolog\tDS-16"
  notes: The final Science supplementary Table S6 maps working_id PLIK to DS_name
    DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1
    positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t\
    7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37"
  notes: The final Science supplementary Table S7 reports a PLIK assay row with a
    Bas26 phage readout and smaller plaques.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t\
    3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37"
  notes: The final Science supplementary Table S7 reports a PLIK assay row with a
    T4 phage readout and a -log(EOP) value of 3.301.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "PLIK\tDS-16\tTrue"
  notes: The final Science supplementary Table S8 maps PLIK to replicated display
    name DS-16.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "PLIK\t2.0\t341.0\tWP_001676492.1\tRelE\t4NRN_A\tmetal-bound toxin; Toxin;\t\
    hhpred_4269994.hhr\t239.0\t335.0\t0.8002\t2024-04-15 00:00:00"
  notes: The final Science supplementary Table S8 reports a RelE HHpred hit for WP_001676492.1
    in PLIK.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "PLIK\t1.0\t656.0\tWP_001676491.1\tABC ATPase\t6QJ0_A\tStructural maintenance\
    \ of chromosomes protein,Structural maintenance of chromosomes protein; condensin\
    \ SMC complex ATPase\thhpred_2524462.hhr\t1.0\t572.0\t0.997\t2024-04-15 00:00:00"
  notes: The final Science supplementary Table S8 reports an ABC ATPase HHpred hit
    for WP_001676491.1 in PLIK.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-16 | 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-16 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-16__DS-16A                                    |                                                  |
    DS-16                  | Custom                  | 500    |'
  notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom
    DS-16 profile.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| DS-16__DS-16B                                    |                                                  |
    DS-16                  | Custom                  | 50     |'
  notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom
    DS-16 profile.
causal_graphs:
- graph_id: ds_16_locus_reduces_phage_plaquing
  title: DS-16 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the two-gene DS-16 locus to
    reduced bacteriophage plaquing without resolving DS-16 component function or molecular
    output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-16 as the validated PLIK transcriptional unit
    with two product accessions, RelE and ABC ATPase HHpred-domain rows, and two DefenseFinder
    DS-16 profile rows. It does not assert native host breadth, exact profile-to-protein
    correspondence, DS-16A or DS-16B molecular activity, trigger, substrate, phage
    breadth, or DefenseFinder rule-level detection criteria.
  nodes:
  - node_id: ds_16_locus
    label: DS-16 locus
    node_type: GENETIC_ELEMENT
    description: A two-gene DefensePredictor-discovered system 16 locus represented
      in the pinned DefenseFinder HMM inventory by DS-16A and DS-16B custom profiles.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced bacteriophage plaquing in cells carrying cloned PLIK.
  - node_id: ds_16_system_trait
    label: DS-16 system
    node_type: TRAIT
    grounding: traitmech:000439
    description: Possession of a genome-encoded DS-16 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_16_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-16/PLIK 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: "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\t\
        DefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing\
        \ protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\t\
        True\tTrue\tStructural defense homolog\tDS-16"
      notes: The final Science supplementary Table S6 maps working_id PLIK to DS_name
        DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1
        positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t\
        7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a PLIK assay row with
        a Bas26 phage readout and smaller plaques.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t\
        3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a PLIK assay row with
        a T4 phage readout and a -log(EOP) value of 3.301.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "PLIK\tDS-16\tTrue"
      notes: The final Science supplementary Table S8 maps PLIK to replicated display
        name DS-16.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-16__DS-16A                                    |                                                  |
        DS-16                  | Custom                  | 500    |'
      notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom
        DS-16 profile.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-16__DS-16B                                    |                                                  |
        DS-16                  | Custom                  | 50     |'
      notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom
        DS-16 profile.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_16_system_trait
    description: DS-16-mediated phage plaquing reduction realizes the DS-16 system
      trait.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\t\
        DefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing\
        \ protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\t\
        True\tTrue\tStructural defense homolog\tDS-16"
      notes: The final Science supplementary Table S6 maps working_id PLIK to DS_name
        DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1
        positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t\
        7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a PLIK assay row with
        a Bas26 phage readout and smaller plaques.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t\
        3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a PLIK assay row with
        a T4 phage readout and a -log(EOP) value of 3.301.
    - 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_16_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-16 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-16 | 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-16 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-16-defensefinder-model-gap
  prompt: Resolve DS-16 native host breadth, exact profile-to-protein mapping, DS-16A/DS-16B
    component activities, RelE and ABC ATPase chemistry, sensitive-phage breadth,
    molecular output, and rule-level DefenseFinder criteria before minting narrower
    DS-16 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-16 as the defensive PLIK transcriptional unit
    and final Science Tables S6/S7/S8 map it to product accessions WP_001676492.1
    and WP_001676491.1, Bas26 and T4 phage readouts, display name DS-16, and RelE/ABC
    ATPase HHpred rows. The pinned DefenseFinder HMM inventory records DS-16A and
    DS-16B custom profile rows. The pinned rules table has no DS-16 row, and the first-pass
    record does not resolve native host breadth, phage breadth, direct profile-to-protein
    correspondence, RelE nuclease or ABC ATPase activity, molecular output, or endogenous
    DS-16 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: "PLIK\tNZ_QOYD01000001.1\tGCF_003333765.1\t-\tTrue\tFalse\tTrue\tTrue\t\
      DefensePredictor hits\t281241\t284220\thypothetical protein, DUF3696 domain-containing\
      \ protein\tWP_001676492.1, WP_001676491.1\t10.6830001978657\t5.517452896464706\t\
      True\tTrue\tStructural defense homolog\tDS-16"
    notes: The final Science supplementary Table S6 maps working_id PLIK to DS_name
      DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1
      positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas26\t2.2\tpLAND\t24-03-12_EV.png\t2400000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB_2.png\t\
      7\t31\tY\t310000000\t0.8888495478773333\t\tTrue\t\tLB\t37"
    notes: The final Science supplementary Table S7 reports a PLIK assay row with
      a Bas26 phage readout and smaller plaques.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "T4\t2.1\tpLAND\t24-03-12_EV.png\t200000000\tPLIK\t24-03-21\t24-03-21_PLIK_REPB.png\t\
      3\t100\t\t100000\t3.3010299956639813\t\tTrue\t\tLB\t37"
    notes: The final Science supplementary Table S7 reports a PLIK assay row with
      a T4 phage readout and a -log(EOP) value of 3.301.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "PLIK\tDS-16\tTrue"
    notes: The final Science supplementary Table S8 maps PLIK to replicated display
      name DS-16.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "PLIK\t2.0\t341.0\tWP_001676492.1\tRelE\t4NRN_A\tmetal-bound toxin; Toxin;\t\
      hhpred_4269994.hhr\t239.0\t335.0\t0.8002\t2024-04-15 00:00:00"
    notes: The final Science supplementary Table S8 reports a RelE HHpred hit for
      WP_001676492.1 in PLIK.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "PLIK\t1.0\t656.0\tWP_001676491.1\tABC ATPase\t6QJ0_A\tStructural maintenance\
      \ of chromosomes protein,Structural maintenance of chromosomes protein; condensin\
      \ SMC complex ATPase\thhpred_2524462.hhr\t1.0\t572.0\t0.997\t2024-04-15 00:00:00"
    notes: The final Science supplementary Table S8 reports an ABC ATPase HHpred hit
      for WP_001676491.1 in PLIK.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-16 | 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-16 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-16__DS-16A                                    |                                                  |
      DS-16                  | Custom                  | 500    |'
    notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom
      DS-16 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| DS-16__DS-16B                                    |                                                  |
      DS-16                  | Custom                  | 50     |'
    notes: The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom
      DS-16 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-16, DS-16A, or DS-16B,
      leaving complete component coverage and rule-level detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_16_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-28'
curation_history:
- timestamp: '2026-09-28T17:24:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-16 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 PLIK transcriptional-unit
    level because RelE/ABC ATPase chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v316
    reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-28T17:24:01Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-16 system canonical_examples and left them empty because DeWeirdt
    et al. directly support cloned PLIK assays in E. coli MG1655 and DefenseFinder
    DS-16 models, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-16 activity. No paid research was used.
  llm_assisted: true