PD-T7-5 system

traitmech:000397 · CLASS · PROPOSED

A phage defense system in which an organism possesses a PD-T7-5 locus represented by DefenseFinder as a single-profile model, PD-T7-5__PD-T7-5, and experimentally linked to SECphi17, T3, and T7 protection when expressed in E. coli.

Trait evidence (10)

DOI:10.1038/s41564-022-01219-4
Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.

Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-5 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).

The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.

The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
The PD-T7-5 system is composed of one protein: PD-T7-5.

The DefenseFinder wiki names PD-T7-5 as a single-protein system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
The PD-T7-5 system in *Shewanella putrefaciens* (GCF_019599085.1, NZ_CP080633) is composed of 1 protein: PD-T7-5 (WP_220590848.1)

The DefenseFinder wiki illustrates a predicted one-protein PD-T7-5 locus in RefSeq assembly GCF_019599085.1 on NZ_CP080633.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7

The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
subgraph Title4[Protects against] SECphi17 T3 T7

The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-T7-5 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\. coli pangenome

The DefenseFinder article registry maps the named PD-T7-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T7-5 PD-T7-5 1 1 PD-T7-5__PD-T7-5

The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T7-5__PD-T7-5 | PD-T7-5__PD-T7-5 | PD-T7-5 | Custom | 90 |

The DefenseFinder HMM inventory records PD-T7-5__PD-T7-5 under the PD-T7-5 system namespace.

PD-T7-5 loci restrict SECphi17, T3, and T7

Conservative system-level sketch linking possession of a PD-T7-5 locus to protection against SECphi17, T3, and T7.

NONMECHANISTIC · The graph captures PD-T7-5 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the PD(D/E)XK effector mechanism unresolved.

Edge evidence

PD-T7-5 locus contributes to SECphi17, T3, and T7 protection RO:0002326
The DefenseFinder wiki links a PD-T7-5 locus from Vassallo et al. to protection against SECphi17, T3, and T7, and DefenseFinder models PD-T7-5 through one mandatory profile.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1). The DefenseFinder wiki describes PD-T7-5 as a single-protein defense system with heterologous E. coli antiphage activity against T7 and T3 plaque-size reduction.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}. The DefenseFinder wiki states that PD-T7-5 molecular mechanism is unresolved and leaves the PD(D/E)XK-mediated DNA degradation interpretation as a hypothesis.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md The PD-T7-5 system is composed of one protein: PD-T7-5. The DefenseFinder wiki names PD-T7-5 as a single-protein system.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md subgraph Title4[Protects against] SECphi17 T3 T7 The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-T7-5 PD-T7-5 1 1 PD-T7-5__PD-T7-5 The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-T7-5__PD-T7-5 | PD-T7-5__PD-T7-5 | PD-T7-5 | Custom | 90 | The DefenseFinder HMM inventory records PD-T7-5__PD-T7-5 under the PD-T7-5 system namespace.
SECphi17, T3, and T7 protection confers PD-T7-5 system METPO:2007700
Protection against SECphi17, T3, and T7 realizes the PD-T7-5 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T7-5 source locus expressed in E. coli against SECphi17, T3, and T7.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md subgraph Title4[Protects against] SECphi17 T3 T7 The DefenseFinder experimental-validation diagram lists SECphi17, T3, and T7 in the PD-T7-5 protects-against subgraph.
PD-T7-5 system is a phage defense system rdfs:subClassOf
PD-T7-5 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-022-01219-4 Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-T7-5 and related conserved phage-defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PD-T7-5 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\. coli pangenome The DefenseFinder article registry maps the named PD-T7-5 system to the Vassallo et al. E. coli pangenome phage-defense preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-T7-5 PD-T7-5 1 1 PD-T7-5__PD-T7-5 The DefenseFinder rules table models PD-T7-5 as a single-profile system requiring PD-T7-5__PD-T7-5.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

PD-T7-5 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
PD-T7-5__PD-T7-5 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

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 PD-T7-5 natural host breadth, direct phage trigger, and PD(D/E)XK effector mechanism before minting narrower PD-T7-5 mechanism traits.

KNOWLEDGE GAP OPEN pd-t7-5-mechanism-gap · raised by codex · 2026-09-27

Attached to causal_graphs#pd_t7_5_locus_restricts_phages

Vassallo et al. support PD-T7-5 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against SECphi17, T3, and T7, and DefenseFinder represents the system with one profile. Natural host breadth, the direct phage trigger, and the PD(D/E)XK effector mechanism remain unresolved.

Evidence

DOI:10.1038/s41564-022-01219-4
Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
The PD-T7-5 system is composed of one protein: PD-T7-5.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-5.md
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T7-5 PD-T7-5 1 1 PD-T7-5__PD-T7-5
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T7-5__PD-T7-5 | PD-T7-5__PD-T7-5 | PD-T7-5 | Custom | 90 |

Curation history

2026-09-27T00:29:55Z · MINTED_TRAITMECH_ID · codex
Minted PD-T7-5 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 replacement placeholder is reserved in proposals/metpo_traitmech_v274.
2026-09-27T00:29:56Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed PD-T7-5 system canonical_examples and left them empty because the current sources support an E. coli accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Shewanella putrefaciens example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T7-5 activity. No paid research was used.