identifier: traitmech:000456
label: DS-33 system
definition: A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered
  system 33 locus cataloged as working transcriptional unit GNAT 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-33
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1126/science.adv7924
- synonym_text: GNAT
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
- synonym_text: DS-33__DS-33
  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: "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\t\
    DefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\t\
    WP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\tTrue\t\
    Predicted novel defense gene\tDS-33"
  notes: The final Science supplementary Table S6 maps working_id GNAT to DS_name
    DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1
    positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
  snippet: "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t24-03-09\t\
    24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\tTrue\t\t\
    \tLB\t37"
  notes: The final Science supplementary Table S7 reports a GNAT assay row with a
    Bas26 phage readout and a -log(EOP) value of 4.699.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "GNAT\tDS-33\tTrue"
  notes: The final Science supplementary Table S8 maps GNAT to replicated display
    name DS-33.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related putative\
    \ DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4\thhpred_9793887.hhr\t\
    25.0\t110.0\t0.5601\t2024-04-16 00:00:00"
  notes: The final Science supplementary Table S8 reports a lower-probability Csa3
    HHpred hit for WP_000354965.1 in GNAT.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
  snippet: "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990 ; MAE_28990/MAE_18760-like\
    \ HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t2024-04-15 00:00:00"
  notes: The final Science supplementary Table S8 reports a high-probability HEPN
    HHpred hit for WP_014639476.1 in GNAT.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: '| DS-33 | 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-33 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-33__DS-33                                     |                                                  |
    DS-33                  | Custom                  | 220    |'
  notes: The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33
    profile.
causal_graphs:
- graph_id: ds_33_locus_reduces_phage_plaquing
  title: DS-33 locus reduces bacteriophage plaquing
  description: Conservative system-level sketch linking the two-gene DS-33 locus to
    reduced bacteriophage plaquing without resolving DS-33 component function or molecular
    output.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures DS-33 as the validated GNAT transcriptional unit
    with two product accessions, a lower-probability Csa3 HHpred row for WP_000354965.1,
    a high-probability HEPN HHpred row for WP_014639476.1, and one DefenseFinder DS-33
    profile row. It does not assert native host breadth, exact profile-to-protein
    correspondence, DS-33 molecular activity, trigger, substrate, complete phage breadth,
    Csa3 or HEPN HHpred-domain interpretation, or DefenseFinder rule-level detection
    criteria.
  nodes:
  - node_id: ds_33_locus
    label: DS-33 locus
    node_type: GENETIC_ELEMENT
    description: A two-gene DefensePredictor-discovered system 33 locus represented
      in the pinned DefenseFinder HMM inventory by one DS-33 custom profile.
  - node_id: reduced_phage_plaquing
    label: reduced bacteriophage plaquing
    node_type: BIOLOGICAL_PROCESS
    description: Reduced bacteriophage plaquing in cells carrying cloned GNAT.
  - node_id: ds_33_system_trait
    label: DS-33 system
    node_type: TRAIT
    grounding: traitmech:000456
    description: Possession of a genome-encoded DS-33 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_33_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: reduced_phage_plaquing
    description: The DS-33/GNAT 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: "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical\
        \ protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\t\
        True\tTrue\tPredicted novel defense gene\tDS-33"
      notes: The final Science supplementary Table S6 maps working_id GNAT to DS_name
        DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1
        positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t\
        24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\t\
        True\t\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a GNAT assay row with
        a Bas26 phage readout and a -log(EOP) value of 4.699.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "GNAT\tDS-33\tTrue"
      notes: The final Science supplementary Table S8 maps GNAT to replicated display
        name DS-33.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related\
        \ putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate,\
        \ cA4\thhpred_9793887.hhr\t25.0\t110.0\t0.5601\t2024-04-16 00:00:00"
      notes: The final Science supplementary Table S8 reports a lower-probability
        Csa3 HHpred hit for WP_000354965.1 in GNAT.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
      snippet: "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990\
        \ ; MAE_28990/MAE_18760-like HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t\
        2024-04-15 00:00:00"
      notes: The final Science supplementary Table S8 reports a high-probability HEPN
        HHpred hit for WP_014639476.1 in GNAT.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| DS-33__DS-33                                     |                                                  |
        DS-33                  | Custom                  | 220    |'
      notes: The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom
        DS-33 profile.
  - subject: reduced_phage_plaquing
    predicate: confers
    predicate_id: METPO:2007700
    object: ds_33_system_trait
    description: DS-33-mediated phage plaquing reduction realizes the DS-33 system
      trait.
    evidence:
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
      snippet: "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\t\
        True\tDefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical\
        \ protein\tWP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\t\
        True\tTrue\tPredicted novel defense gene\tDS-33"
      notes: The final Science supplementary Table S6 maps working_id GNAT to DS_name
        DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1
        positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
    - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
      snippet: "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t\
        24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\t\
        True\t\t\tLB\t37"
      notes: The final Science supplementary Table S7 reports a GNAT assay row with
        a Bas26 phage readout and a -log(EOP) value of 4.699.
    - 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_33_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: DS-33 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-33 | 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-33 source key to
        the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has
        since been published in Science.
discussions:
- discussion_id: ds-33-defensefinder-model-gap
  prompt: Resolve DS-33 native host breadth, exact component activities, profile-to-protein
    mapping, Csa3 and HEPN HHpred-domain interpretation, complete phage breadth, molecular
    output, and rule-level DefenseFinder criteria before minting narrower DS-33 mechanism
    children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: DeWeirdt et al. support DS-33 as the defensive GNAT transcriptional unit
    and final Science Tables S6/S7/S8 map it to two product accessions, a Bas26 phage
    readout, display name DS-33, and two HHpred rows. The pinned DefenseFinder HMM
    inventory records one DS-33 custom profile row. The pinned rules table has no
    DS-33 row, and the first-pass record does not resolve native host breadth, complete
    phage breadth, direct profile-to-protein correspondence, component activities,
    molecular output, or endogenous DS-33 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: "GNAT\tNZ_QOWT01000046.1\tGCF_003334765.1\t+\tTrue\tFalse\tFalse\tTrue\t\
      DefensePredictor hits\t6922\t8901\thypothetical protein, hypothetical protein\t\
      WP_014639476.1, WP_000354965.1\t9.45173070144912\t3.204412762840645\tTrue\t\
      True\tPredicted novel defense gene\tDS-33"
    notes: The final Science supplementary Table S6 maps working_id GNAT to DS_name
      DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1
      positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
    snippet: "Bas26\t1.2\tpLAND\t24-03-08_EV_HHHD_PIN2_CRDO.png\t500000000\tGNAT\t\
      24-03-09\t24-03-09_GNAT_NADR_D390_DRAT.png\t2\t100\tY\t10000\t4.698970004336019\t\
      True\t\t\tLB\t37"
    notes: The final Science supplementary Table S7 reports a GNAT assay row with
      a Bas26 phage readout and a -log(EOP) value of 4.699.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "GNAT\tDS-33\tTrue"
    notes: The final Science supplementary Table S8 maps GNAT to replicated display
      name DS-33.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "GNAT\t2.0\t333.0\tWP_000354965.1\tCsa3\t6W11_B\tCRISPR locus-related\
      \ putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate,\
      \ cA4\thhpred_9793887.hhr\t25.0\t110.0\t0.5601\t2024-04-16 00:00:00"
    notes: The final Science supplementary Table S8 reports a lower-probability Csa3
      HHpred hit for WP_000354965.1 in GNAT.
  - reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
    snippet: "GNAT\t1.0\t320.0\tWP_014639476.1\tHEPN\tPF18737.5\tHEPN_MAE_28990 ;\
      \ MAE_28990/MAE_18760-like HEPN\thhpred_9884029.hhr\t144.0\t306.0\t0.9842\t\
      2024-04-15 00:00:00"
    notes: The final Science supplementary Table S8 reports a high-probability HEPN
      HHpred hit for WP_014639476.1 in GNAT.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: '| DS-33 | 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-33 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-33__DS-33                                     |                                                  |
      DS-33                  | Custom                  | 220    |'
    notes: The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom
      DS-33 profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: The pinned DefenseFinder rules table does not list DS-33, leaving rule-level
      detection criteria unresolved.
  attaches_to:
  - causal_graphs#ds_33_locus_reduces_phage_plaquing
  posed_by: codex
  posed_date: '2026-09-29'
curation_history:
- timestamp: '2026-09-29T08:03:43Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted DS-33 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 GNAT transcriptional-unit
    level because Csa3 and HEPN activity and rule rows remain unresolved, and proposals/metpo_traitmech_v333
    reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-29T08:03:44Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed DS-33 system canonical_examples and left them empty because DeWeirdt
    et al. directly support cloned GNAT assays in E. coli MG1655 and a DefenseFinder
    DS-33 model, but not a direct named native microbial isolate exemplar with experimentally
    verified endogenous DS-33 activity. No paid research was used.
  llm_assisted: true