identifier: traitmech:000476
label: PD-T2-1 system
definition: A phage defense system in which an organism possesses a two-gene PD-T2-1
  operon whose expression was experimentally linked to protection against T2, T6,
  Bas18, T4, and T5 phages.
definition_source: DOI:10.1038/s41564-025-02239-6
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-T2-1
  synonym_type: EXACT_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
- synonym_text: PD-T2–1
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1038/s41564-025-02239-6
- synonym_text: geneAB operon
  synonym_type: RELATED_SYNONYM
  source: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
evidence:
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: Two phage proteins were further investigated, revealing T7 gp17 and additional
    tail fiber proteins activated the undescribed antiphage system PD-T2–1 and identifying
    λ gpE major capsid protein activated the antiphage system Avs8.
  notes: Goedecke et al. report that T7 gp17 and additional tail fiber proteins activated
    the previously undescribed PD-T2-1 antiphage system.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: Sequencing the transposon insertion site of mutants that did grow revealed
    28 out of 48 mutants contained transposons that disrupted a two-gene operon of
    unknown function
  notes: ECOR03 transposon mutants that escaped T7 gp17-mediated growth inhibition
    were enriched for insertions disrupting the same unknown two-gene operon.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: Operon structure of phage defense against T2 system 1 (PD-T2–1). Transposon
    insertions identified in mutant ECOR03 expressing T7 gp17 are indicated with triangles.
    A predicted transmembrane domain (TM) for PD-T2–1A, accession numbers, and the
    length of each protein in amino acids (aa) are shown.
  notes: The PD-T2-1 operon figure identifies transposon insertions, the predicted
    transmembrane domain in PD-T2-1A, and the protein accessions used in the study.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: GeneAB conferred >100-fold protection against phages T2, T6, and Bas18,
    and approximately 10-fold protection against phages T4 and T5
  notes: Expression of the operon in MG1655 protected against T2, T6, Bas18, T4, and
    T5 in phage-challenge assays.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: These findings led us to rename the geneAB operon phage defense against
    T2 system 1 (PD-T2–1)
  notes: Goedecke et al. renamed the placeholder geneAB operon phage defense against
    T2 system 1.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: Transformation efficiency assays revealed that PD-T2–1 also selectively
    inhibited bacterial growth when T2 gp37, T2 gp34, and T2 gp12 were co-expressed
  notes: PD-T2-1 also selectively inhibited growth when the T2 tail-fiber genes gp37,
    gp34, and gp12 were expressed.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: These results indicate PD-T2–1 does not function as a canonical toxin-antitoxin
    system.
  notes: Single-gene expression experiments argue against PD-T2-1 as a canonical toxin-antitoxin
    system.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: 'ECOR03 PD-T2–1A: RCR47252.1; WP_075861856.1'
  notes: The Methods section reports the ECOR03 PD-T2-1A RefSeq and nonredundant protein
    accessions used in the article.
- reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
  snippet: 'Nucleotide coordinates for PD-T2–1 in ECOR03 (accession QOWO01000016):
    10,064–11,256'
  notes: The extended-data figure caption places the ECOR03 PD-T2-1 locus on nucleotide
    record QOWO01000016.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-T2-1 | 10\.1101/2025\.07\.02\.662641 | Identifying phage proteins that
    activate the bacterial innate immune system
  notes: The pinned DefenseFinder article registry maps the named PD-T2-1 system to
    the Goedecke et al. preprint.
causal_graphs:
- graph_id: pd_t2_1_locus_phage_protection
  title: PD-T2-1 loci protect against multiple phages
  description: Conservative system-level sketch linking a PD-T2-1 locus to experimentally
    measured T2, T6, Bas18, T4, and T5 protection.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-T2-1 as a named phage-defense system in the final
    Goedecke et al. article and pinned DefenseFinder article registry while leaving
    the direct sensor or output mechanism, native host breadth, accession-level protein
    examples, profile-to-protein mapping, and exact DefenseFinder HMM/rules detection
    criteria unresolved.
  nodes:
  - node_id: pd_t2_1_locus
    label: PD-T2-1 locus
    node_type: GENETIC_ELEMENT
    description: A two-gene phage-defense locus corresponding to the ECOR03 operon
      renamed PD-T2-1.
  - node_id: pd_t2_1_listed_phage_protection
    label: T2, T6, Bas18, T4, and T5 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T6, Bas18, T4, and T5 after PD-T2-1 expression
      in MG1655.
  - node_id: pd_t2_1_system_trait
    label: PD-T2-1 system
    node_type: TRAIT
    grounding: traitmech:000476
    description: Possession of a genome-encoded PD-T2-1 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: pd_t2_1_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_t2_1_listed_phage_protection
    description: Expression of the PD-T2-1 operon in MG1655 protected against phages
      T2, T6, Bas18, T4, and T5.
    evidence:
    - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
      snippet: GeneAB conferred >100-fold protection against phages T2, T6, and Bas18,
        and approximately 10-fold protection against phages T4 and T5
      notes: Goedecke et al. challenged MG1655 expressing the PD-T2-1 operon with
        diverse phages and measured protection.
    - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
      snippet: These findings led us to rename the geneAB operon phage defense against
        T2 system 1 (PD-T2–1)
      notes: Goedecke et al. renamed the two-gene geneAB operon PD-T2-1.
  - subject: pd_t2_1_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_t2_1_system_trait
    description: Protection against T2, T6, Bas18, T4, and T5 realizes the PD-T2-1
      phage-defense-system trait.
    evidence:
    - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
      snippet: GeneAB conferred >100-fold protection against phages T2, T6, and Bas18,
        and approximately 10-fold protection against phages T4 and T5
      notes: The PD-T2-1 operon conferred phage protection when expressed in MG1655.
  - subject: pd_t2_1_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-T2-1 system possession is a phage-defense system trait.
    evidence:
    - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
      snippet: Two phage proteins were further investigated, revealing T7 gp17 and
        additional tail fiber proteins activated the undescribed antiphage system
        PD-T2–1 and identifying λ gpE major capsid protein activated the antiphage
        system Avs8.
      notes: Goedecke et al. identify PD-T2-1 as an undescribed antiphage system.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-T2-1 | 10\.1101/2025\.07\.02\.662641 | Identifying phage proteins
        that activate the bacterial innate immune system
      notes: The pinned DefenseFinder article registry maps the named PD-T2-1 system
        to the Goedecke et al. preprint.
discussions:
- discussion_id: pd-t2-1-mechanism-and-model-coverage-gap
  prompt: Resolve the PD-T2-1 direct sensor, effector output, native host breadth,
    and DefenseFinder HMM/rules model coverage before minting narrower PD-T2-1 mechanism
    or protein-component traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The final Goedecke et al. article supports PD-T2-1 as a two-gene operon
    activated by multiple phage tail-fiber proteins, links heterologous expression
    to protection against T2, T6, Bas18, T4, and T5, and argues that the system is
    not a canonical toxin-antitoxin system. The pinned DefenseFinder article registry
    names PD-T2-1 and maps it to the Goedecke et al. preprint, but the pinned HMM
    inventory and rules table do not contain PD-T2-1 rows, leaving profile coverage
    and detection criteria unresolved.
  evidence:
  - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    snippet: Transformation efficiency assays revealed that PD-T2–1 also selectively
      inhibited bacterial growth when T2 gp37, T2 gp34, and T2 gp12 were co-expressed
    notes: PD-T2-1 responded to multiple T2 tail-fiber proteins in transformation-efficiency
      assays.
  - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    snippet: These results indicate PD-T2–1 does not function as a canonical toxin-antitoxin
      system.
    notes: The PD-T2-1A/PD-T2-1B single-gene assays argue against a canonical toxin-antitoxin
      mechanism.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    snippet: PD-T2-1 | 10\.1101/2025\.07\.02\.662641 | Identifying phage proteins
      that activate the bacterial innate immune system
    notes: The pinned DefenseFinder article registry maps the named PD-T2-1 system
      to the Goedecke et al. preprint.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    notes: No PD-T2-1 or PD-T2-1-prefixed HMM inventory row was present in the pinned
      DefenseFinder model file.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    notes: No PD-T2-1 rule row was present in the pinned DefenseFinder rules table.
  attaches_to:
  - causal_graphs#pd_t2_1_locus_phage_protection
  posed_by: codex
  posed_date: '2026-09-29'
curation_history:
- timestamp: '2026-09-29T22:58:06Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-T2-1 system as a DOI- and DefenseFinder-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. The proposals/metpo_traitmech_v353
    cohort reserves the replacement placeholder.
  llm_assisted: true
- timestamp: '2026-09-29T22:58:07Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-T2-1 canonical_examples and left them empty because ECOR03
    supports native discovery and locus coordinates without a verified NCBITaxon strain
    CURIE, while heterologous MG1655 phage-challenge assays do not by themselves support
    an endogenous named isolate exemplar. No paid research was used.
  llm_assisted: true