PXD000219

PXD000219 is an original dataset announced via ProteomeXchange.

Title	Protein abundance comparison of human cells infected with Shigella flexneri over different time periods
Description	The enteroinvasive bacterium Shigella flexneri invades the intestinal epithelium of humans. During infection, several injected effector proteins promote bacterial internalization, and interfere with multiple host cell responses. To obtain a systems-level overview of host signaling during infection, we analyzed the global dynamics of protein phosphorylation by LC-MS/MS and identified several hundred of proteins undergoing a phosphorylation change during the first hours of infection. Functional bioinformatic analysis revealed that they were mostly related to the cytoskeleton, transcription, signal transduction, and cell cycle. Fuzzy c-means clustering identified six temporal profiles of phosphorylation and a functional module composed of ATM-phosphorylated proteins related to genotoxic stress. Pathway enrichment analysis defined mTOR as the most overrepresented pathway. We showed that mTOR complex 1 and 2 were required for S6 kinase and AKT activation, respectively. Comparison with a published phosphoproteome of Salmonella typhimurium-infected cells (PMID:21934108, PRIDE experiment accessions 18477 and 18485) revealed a large subset of co-regulated phosphoproteins. Finally, we showed that S. flexneri effector OspF affected the phosphorylation of several hundred proteins, thereby demonstrating the wide-reaching impact of a single bacterial effector on the host signaling network.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_08:54:10.306.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000219
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-22 02:36:07	ID requested
1	2017-01-23 10:12:29	announced
⏵ 2	2024-10-07 08:54:11	announced	2024-10-07: Updated project metadata.

Schmutz C, Ahrn, é E, Kasper CA, Tschon T, Sorg I, Dreier RF, Schmidt A, Arrieumerlou C, Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Mol Cell Proteomics, 12(10):2952-68(2013) [pubmed]

10.6019/PXD000219;

10.1074/mcp.M113.029918;

submitter keyword: Infection, Phosphoproteomics, S. flexneri

Alexander Schmidt
contact affiliation	Biozentrum, University of Basel
contact email	alex.schmidt@unibas.ch
lab head
Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
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/2017/01/PXD000219

PRIDE project URI

• PRIDE
  1. PXD000219
     1. Label: PRIDE project
     2. Name: Protein abundance comparison of human cells infected with Shigella flexneri over different time periods