PD-T4-8 system

traitmech:000393 · CLASS · PROPOSED

A phage defense system in which an organism possesses a PD-T4-8 locus represented by DefenseFinder as a single-profile model, PD-T4-8__PD-T4-8, and experimentally linked to T2, T4, T6, SECphi18, and SECphi27 protection when expressed in E. coli.

Trait evidence (9)

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-T4-8 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.

The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
The PD-T4-8 is composed of 1 protein: PD-T4-8.

The DefenseFinder wiki names PD-T4-8 as a single-protein system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
The PD-T4-8 system in *Algoriphagus sp. Y33* (GCF_014838715.1, NZ_CP061947) is composed of 1 protein: PD-T4-8 (WP_144603961.1)

The DefenseFinder wiki illustrates a predicted PD-T4-8 locus in RefSeq assembly GCF_014838715.1 on NZ_CP061947.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.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/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27

The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
subgraph Title4[Protects against] T2 T4 T6 SECphi18 SECphi27

The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-T4-8 | 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-T4-8 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-T4-8 PD-T4-8 1 1 PD-T4-8__PD-T4-8

The DefenseFinder rules table models PD-T4-8 as a single-profile system requiring PD-T4-8__PD-T4-8.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-8__PD-T4-8 | PD-T4-8__PD-T4-8 | PD-T4-8 | Custom | 80 |

The DefenseFinder HMM inventory records PD-T4-8__PD-T4-8 under the PD-T4-8 system namespace.

PD-T4-8 loci restrict T2, T4, T6, SECphi18, and SECphi27

Conservative system-level sketch linking possession of a PD-T4-8 locus to protection against T2, T4, T6, SECphi18, and SECphi27.

NONMECHANISTIC · The graph captures PD-T4-8 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and effector logic unresolved.

Edge evidence

PD-T4-8 locus contributes to T2, T4, T6, SECphi18, and SECphi27 protection RO:0002326
The DefenseFinder wiki links a PD-T4-8 locus from Vassallo et al. to protection against T2, T4, T6, SECphi18, and SECphi27, and DefenseFinder models PD-T4-8 through one mandatory profile.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27. The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md The PD-T4-8 is composed of 1 protein: PD-T4-8. The DefenseFinder wiki names PD-T4-8 as a single-protein system.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.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/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md subgraph Title4[Protects against] T2 T4 T6 SECphi18 SECphi27 The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-T4-8 PD-T4-8 1 1 PD-T4-8__PD-T4-8 The DefenseFinder rules table models PD-T4-8 as a single-profile system requiring PD-T4-8__PD-T4-8.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-T4-8__PD-T4-8 | PD-T4-8__PD-T4-8 | PD-T4-8 | Custom | 80 | The DefenseFinder HMM inventory records PD-T4-8__PD-T4-8 under the PD-T4-8 system namespace.
T2, T4, T6, SECphi18, and SECphi27 protection confers PD-T4-8 system METPO:2007700
Protection against T2, T4, T6, SECphi18, and SECphi27 realizes the PD-T4-8 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27. The DefenseFinder wiki reports that PD-T4-8 contains a DUF4263 domain and that the E. coli RCP52534.1 locus confers resistance against T2, T4, T6, SECphi18, and SECphi27.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.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/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-8 source locus expressed in E. coli against T2, T4, T6, SECphi18, and SECphi27.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md subgraph Title4[Protects against] T2 T4 T6 SECphi18 SECphi27 The DefenseFinder experimental-validation diagram lists T2, T4, T6, SECphi18, and SECphi27 in the PD-T4-8 protects-against subgraph.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

PD-T4-8 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
PD-T4-8__PD-T4-8 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-T4-8 natural host breadth, direct phage trigger, and effector logic before minting narrower PD-T4-8 mechanism traits.

KNOWLEDGE GAP OPEN pd-t4-8-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_t4_8_locus_restricts_t2_t4_t6_secphi18_and_secphi27

Vassallo et al. support PD-T4-8 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, SECphi18, and SECphi27, and DefenseFinder represents the system with one mandatory profile. Natural host breadth, the direct phage trigger, and effector logic 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-t4-8.md
PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.md
The PD-T4-8 is composed of 1 protein: PD-T4-8.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-8.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/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T4-8 PD-T4-8 1 1 PD-T4-8__PD-T4-8
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-8__PD-T4-8 | PD-T4-8__PD-T4-8 | PD-T4-8 | Custom | 80 |

Curation history

2026-09-26T20:08:00Z · MINTED_TRAITMECH_ID · codex
Minted PD-T4-8 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_v270.
2026-09-26T20:08:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed PD-T4-8 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 Algoriphagus example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-8 activity. No paid research was used.