PfiAT system

traitmech:000365 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Pf4 prophage-encoded PfiAT toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring PfiAT__PfiA and PfiAT__PfiT.

Trait evidence (8)

PMID:32246813
we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair.

Li et al. experimentally identify PA0729 and Rorf0727 in the Pf4 prophage as a PfiT/PfiA type II toxin-antitoxin pair.
PMID:32246813
Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production.

Li et al. show that deleting pfiT increases Pf4 phage production.
PMID:32246813
We thus suggest the toxin PA0729 be named PfiT for Pf4 inhibition toxin and Rorf0727 be named PfiA for PfiT antitoxin.

Li et al. name PA0729 as PfiT and Rorf0727 as PfiA.
PMID:32246813
Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements.

Li et al. frame Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa

The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PfiAT PfiAT 2 2 PfiAT__PfiA, PfiAT__PfiT

The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PfiAT__PfiA | PfiAT__PfiA | PfiAT | Custom | 20 |

The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PfiAT__PfiT | PfiAT__PfiT | PfiAT | Custom | 20 |

The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT.

PfiAT loci regulate Pf4 prophage production

Conservative system-level sketch linking possession of a PfiAT locus to PfiT/PfiA-dependent regulation of Pf4 phage production and immunity without asserting the cellular PfiT toxin target or natural host breadth.

NONMECHANISTIC · The graph captures PfiAT as a named DefenseFinder two-profile Pf prophage system while leaving natural host breadth, the cellular target of PfiT in Pseudomonas, Pf4 phage-immunity coupling, and PfiAT profile-to-activity mapping unresolved.

Edge evidence

PfiAT locus contributes to Pf4 phage production regulation RO:0002326
Li et al. identify the Pf4 PA0729 and Rorf0727 locus as a PfiT/PfiA toxin-antitoxin pair whose pfiT toxin gene inhibits Pf4 production, and DefenseFinder models PfiAT as a two-profile system.
- PMID:32246813 we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair. Li et al. experimentally identify PA0729 and Rorf0727 as a PfiT/PfiA toxin-antitoxin pair near the right attachment site of Pf4.
- PMID:32246813 Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production. Li et al. show that pfiT inhibits Pf4 phage production.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PfiAT PfiAT 2 2 PfiAT__PfiA, PfiAT__PfiT The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PfiAT__PfiA | PfiAT__PfiA | PfiAT | Custom | 20 | The DefenseFinder HMM inventory records PfiAT__PfiA under PfiAT.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PfiAT__PfiT | PfiAT__PfiT | PfiAT | Custom | 20 | The DefenseFinder HMM inventory records PfiAT__PfiT under PfiAT.
Pf4 phage production regulation confers PfiAT system METPO:2007700
PfiT/PfiA-dependent regulation of Pf4 phage production and immunity realizes the PfiAT system trait.
- PMID:32246813 Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements. Li et al. support Pf prophage toxin-antitoxin systems as regulators of phage production and phage immunity.
PfiAT system is a phage defense system rdfs:subClassOf
PfiAT system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PfiAT | 10\.1111/1751-7915\.13570 | Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa The DefenseFinder article registry maps the named PfiAT system to Li et al.'s Pf4 prophage PfiT/PfiA paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PfiAT PfiAT 2 2 PfiAT__PfiA, PfiAT__PfiT The DefenseFinder rules table models PfiAT as a two-profile system requiring the PfiAT__PfiA and PfiAT__PfiT profiles.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1111/1751-7915.13570

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

PfiAT RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PfiAT__PfiA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
PfiAT__PfiT 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 natural PfiAT host breadth, the PfiT cellular target in Pseudomonas, Pf prophage production and immunity coupling, and PfiAT profile-to-activity mapping before minting narrower PfiAT mechanism children.

KNOWLEDGE GAP OPEN pfiat-mechanism-gap · raised by codex · 2026-09-22

Attached to causal_graphs#pfiat_locus_regulates_pf4_phage

Li et al. support PA0729/PfiT and Rorf0727/PfiA in the Pf4 prophage as a type II toxin-antitoxin pair that regulates Pf4 production and phage immunity, and DefenseFinder models PfiAT as a two-profile system with PfiAT__PfiA and PfiAT__PfiT markers. Natural host breadth, the cellular target of PfiT, Pf4 immunity coupling, and profile-to-activity mapping remain unresolved.

Evidence

PMID:32246813
Homologs of PfiT are also found in other Pseudomonas strains, and the cellular target of PfiT in Pseudomonas will be investigated in future studies.

Curation history

2026-09-22T12:25:36Z · MINTED_TRAITMECH_ID · codex
Minted PfiAT 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; the replacement placeholder is reserved in proposals/metpo_traitmech_v242.
2026-09-22T12:25:37Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed the PfiAT canonical_examples gap and left canonical_examples empty: the current evidence supports the Pf4 prophage PfiT/PfiA toxin-antitoxin pair, its control of Pf4 phage production and immunity, and the pinned DefenseFinder PfiAT profiles, but does not cite a directly observed natural microbial taxon with a source-backed PfiAT locus broad enough for a canonical example. No paid research was used.