TraitMech

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PD-T2-1 system

traitmech:000476 · CLASS · PROPOSED

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.

Trait evidence (10)

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    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.

    Goedecke et al. report that T7 gp17 and additional tail fiber proteins activated the previously undescribed PD-T2-1 antiphage system.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    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

    ECOR03 transposon mutants that escaped T7 gp17-mediated growth inhibition were enriched for insertions disrupting the same unknown two-gene operon.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    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.

    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.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5

    Expression of the operon in MG1655 protected against T2, T6, Bas18, T4, and T5 in phage-challenge assays.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    These findings led us to rename the geneAB operon phage defense against T2 system 1 (PD-T2–1)

    Goedecke et al. renamed the placeholder geneAB operon phage defense against T2 system 1.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    Transformation efficiency assays revealed that PD-T2–1 also selectively inhibited bacterial growth when T2 gp37, T2 gp34, and T2 gp12 were co-expressed

    PD-T2-1 also selectively inhibited growth when the T2 tail-fiber genes gp37, gp34, and gp12 were expressed.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    These results indicate PD-T2–1 does not function as a canonical toxin-antitoxin system.

    Single-gene expression experiments argue against PD-T2-1 as a canonical toxin-antitoxin system.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    ECOR03 PD-T2–1A: RCR47252.1; WP_075861856.1

    The Methods section reports the ECOR03 PD-T2-1A RefSeq and nonredundant protein accessions used in the article.

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/
    Nucleotide coordinates for PD-T2–1 in ECOR03 (accession QOWO01000016): 10,064–11,256

    The extended-data figure caption places the ECOR03 PD-T2-1 locus on nucleotide record QOWO01000016.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    PD-T2-1 | 10\.1101/2025\.07\.02\.662641 | Identifying phage proteins that activate the bacterial innate immune system

    The pinned DefenseFinder article registry maps the named PD-T2-1 system to the Goedecke et al. preprint.

PD-T2-1 loci protect against multiple phages

Conservative system-level sketch linking a PD-T2-1 locus to experimentally measured T2, T6, Bas18, T4, and T5 protection.

NONMECHANISTIC · 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.

PD-T2-1 loci protect against multiple phages Interactive directed graph showing evidence-backed causal relationships for PD-T2-1 system.

Edge evidence

  • PD-T2-1 locus contributes to T2, T6, Bas18, T4, and T5 protection RO:0002326

    Expression of the PD-T2-1 operon in MG1655 protected against phages T2, T6, Bas18, T4, and T5.

    • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/ GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5 Goedecke et al. challenged MG1655 expressing the PD-T2-1 operon with diverse phages and measured protection.
    • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/ These findings led us to rename the geneAB operon phage defense against T2 system 1 (PD-T2–1) Goedecke et al. renamed the two-gene geneAB operon PD-T2-1.
  • T2, T6, Bas18, T4, and T5 protection confers PD-T2-1 system METPO:2007700

    Protection against T2, T6, Bas18, T4, and T5 realizes the PD-T2-1 phage-defense-system trait.

    • https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/ GeneAB conferred >100-fold protection against phages T2, T6, and Bas18, and approximately 10-fold protection against phages T4 and T5 The PD-T2-1 operon conferred phage protection when expressed in MG1655.
  • PD-T2-1 system is a phage defense system rdfs:subClassOf

    PD-T2-1 system possession is a phage-defense system trait.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41564-025-02239-6

Parent traits (1)

Synonyms (3)

  • PD-T2-1 EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  • PD-T2–1 EXACT_SYNONYM · DOI:10.1038/s41564-025-02239-6
  • geneAB operon RELATED_SYNONYM · https://pmc.ncbi.nlm.nih.gov/articles/PMC12875140/

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN pd-t2-1-mechanism-and-model-coverage-gap · raised by codex · 2026-09-29

Attached to causal_graphs#pd_t2_1_locus_phage_protection

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.