PXD075006-1

PXD075006 is an original dataset announced via ProteomeXchange.

Title	identification of UFM1-dependent host effectors binding to Shigella flexneri in infectect HeLa cells
Description	Host cells contest invasion by intracellular bacterial pathogens with multiple strategies that recognise and / or damage the bacterial surface. To identify novel host defence factors targeted to intracellular bacteria, we developed a versatile proximity biotinylation approach coupled to quantitative mass spectrometry that maps the host-bacterial interface during infection. Using this method, we discovered that intracellular Shigella and Salmonella become targeted by UFM1-protein ligase 1 (UFL1), an E3 ligase that catalyses the covalent attachment of Ubiquitin-fold modifier 1 (UFM1) to target substrates in a process called UFMylation. We show that Shigella antagonises UFMylation in a dual manner: first, using its lipopolysaccharide (LPS) to shield from UFL1 recruitment; second, preventing UFM1 decoration by the bacterial effector IpaH9.8. Absence of UFMylation leads to an increase of bacterial burden in both human cells and zebrafish larvae, suggesting that UFMylation is a highly conserved antibacterial pathway. Contrary to canonical ubiquitylation, the protective role of UFMylation is independent of autophagy. Here, we used an proteomics-based approach to host effector binding to Shigella in human infected cells. This allowed to confirm UFM1 recruitment to Shigella surface and to identify host effector binding to Shigella in a UFM1-dependent matter. This result reveals potential UFM1 protein substrates on the surface of Shigella in infetec human cells. To do so, we performed siRNA knockdown against UFM1 in HeLa cells prior to infection with the hyperinvasive Shigella flexneri afaI strain considered as the wild-type strain. Alternatively, HeLa cells were infected with S. flexneri ΔrfaCΔipaH9.8 considered as mutant. There were four biological groups with each four replicates: HeLa cells with siUFM1 with wild-type S. flexneri, HeLa cells with non-targeting siRNA with wild-type S. flexneri, siUFM1 with Shigella mutant and non-targeting siRNA with Shigella mutant.
HostingRepository	PRIDE
AnnounceDate	2026-08-17
AnnouncementXML	Submission_2026-08-17_03:31:05.373.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabien Thery
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Shigella flexneri; NCBI TaxID: NEWT:623;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-27 16:40:32	ID requested
⏵ 1	2026-08-17 03:31:05	announced

Dataset with its publication pending

submitter keyword: innate immunity, Shigella flexneri, UFM1

Prof. Francis Impens
contact affiliation	VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium. UGent Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde, 9052 Ghent, Belgium.
contact email	francis.impens@vib-ugent.be
lab head
Fabien Thery
contact affiliation	VIB-UGent
contact email	fabien.thery91@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/2026/08/PXD075006

PRIDE project URI

• PRIDE
  1. PXD075006
     1. Label: PRIDE project
     2. Name: identification of UFM1-dependent host effectors binding to Shigella flexneri in infectect HeLa cells