PXD063439

PXD063439 is an original dataset announced via ProteomeXchange.

Title	Broad and specific anti-defense genes in bacteriophage genomes
Description	Bacteria and bacteriophages have been engaged in a relentless evolutionary arms race, driving a rapid evolution of bacterial defense mechanisms and leading to their scattered distribution across genomes. We hypothesized that the variability in defense systems presence in bacterial genomes leads to equally variable counter-defense repertoires in phage genomes. To test this, we analyzed the variable regions in Pseudomonas model phages of the Pbunavirus genus, uncovering five anti-defense genes inhibiting Zorya type I, RADAR, Hypnos, Druantia type I and III, and Thoeris type III. Remarkably, a typical Pbunavirus encodes up to five known anti-defense genes, some inhibiting four unrelated defense systems with distinct nucleic acid-targeting mechanisms. Structural searches revealed that these broad-acting inhibitors are encoded across diverse phage taxa infecting multiple bacterial hosts. The presence of both broad and specific inhibitors suggests that defense systems exert a strong selective pressure, and their utility presents opportunities to improve phage-based therapeutics.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-23_01:00:51.577.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Konstantinos Kalogeropoulos
SpeciesList	scientific name: Pseudomonas aeruginosa AES-1R; NCBI TaxID: NEWT:1000561; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-29 04:45:26	ID requested
⏵ 1	2026-02-23 01:00:52	announced

10.1016/j.chom.2025.06.010;

Costa AR, van den Berg DF, Esser JQ, van den Bossche H, Pozhydaieva N, Kalogeropoulos K, Brouns SJJ, Bacteriophage genomes encode both broad and specific counter-defense repertoires to overcome bacterial defense systems. Cell Host Microbe, 33(7):1161-1172.e5(2025) [pubmed]

submitter keyword: bacterial immunity, defense systems,bacteriophage, DIA proteomics

Stan J.J. Brouns
contact affiliation	Department of Bionanoscience, Delft University of Technology
contact email	s.j.j.brouns@tudelft.nl
lab head
Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	konskalogero@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD063439

PRIDE project URI

• PRIDE
  1. PXD063439
     1. Label: PRIDE project
     2. Name: Broad and specific anti-defense genes in bacteriophage genomes