PXD072185-1

PXD072185 is an original dataset announced via ProteomeXchange.

Title	Defining the essential genome of diverse phages with Phage Tn-seq
Description	Phages are important drivers of bacterial evolution with therapeutic potential as antimicrobials. However, gaps in our understanding of phages and ability to rapidly engineer them with new genetic cargo hinders progress towards phage-based therapies. To address the lack of unbiased, genome-wide mutational tools for phages, we developed transposon mutagenesis employing CRISPR-anti-CRISPR (Acr)-based selection and deep-sequencing (Phage Tn-seq). Transposon mutagenesis was effective for phages with unmodified or hypermodified genomes and a jumbo phage that protects its DNA within a nucleus. Phage Tn-seq enabled phage gene essentiality assignment consistent with structural proteomics and core gene conservation. Insertion biases allowed prediction of transcriptional direction and early injected phage DNA regions. We exploited the method to rapidly deliver new cargo to phage genomes in just a few days and used an AI-designed Acr to expand the phage transposon toolbox. Phage Tn-seq is versatile tool to advance our understanding and applications of phages.
HostingRepository	PRIDE
AnnounceDate	2026-07-30
AnnouncementXML	Submission_2026-07-30_13:12:47.999.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Torsten Kleffmann
SpeciesList	scientific name: Prodigiosinella confusarubida; NCBI TaxID: NEWT:104623;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-18 22:06:53	ID requested
⏵ 1	2026-07-30 13:12:48	announced

Dataset with its publication pending

submitter keyword: phage proteomics,phage transposon mutagenesis

Peter Fineran
contact affiliation	Department of Microbiology and Immunology, University of Otago, New Zealand
contact email	peter.fineran@otago.ac.nz
lab head
Torsten Kleffmann
contact affiliation	Department of Biochemistry, University of Otago
contact email	torsten.kleffmann@otago.ac.nz
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/2026/07/PXD072185

PRIDE project URI

• PRIDE
  1. PXD072185
     1. Label: PRIDE project
     2. Name: Defining the essential genome of diverse phages with Phage Tn-seq