PXD015660-1

PXD015660 is an original dataset announced via ProteomeXchange.

Title	Proteome analysis of HeLa cells knocked down for EXT1 expression
Description	Exostosin-1 (EXT1) is an ER-resident glycosyltransferase known to polymerize heparan sulfate chain by sequential addition of glucuronic acid and N-acetylglucosamine molecules. This reaction results in heavily glycosylated proteoglycans (PG) at the plasma membrane, which form cell-type specific complexes and play vital roles in cell-cell and cell-pathogens interactions, cell growth, plasticity and proliferation in the local tissue environment. Different evolutionary forces drive the structure and function of protein glycosylation between the inside and outside of the plasma membrane, and an understanding of how the proteome composition of internal cell membranes is regulated remains a fundamental question in biology. In addition, potential interplays between whole cell proteome and membrane composition are completely unknown. We performed EXT1 knockdown in HeLa cells using shRNA, isolated ER microsomes, performed label-free mass spectrometry, and processed the data with byonic 3.5 software to identify glycoproteins. We identified a total of 1080 proteins, 226 with altered expression, 51 phosphoproteins, 25 O-glycosylated and 97 N-glycosylated membrane proteins. We also performed stable isotope labeling amino acids in cell culture comparing proteomes from HeLa knocked down for EXT1 and control cells. We identified a total 5215 proteins, with 3713 proteins having a SILAC ratio and 396 proteins out of total with a significant p-value (p-value <0.05). Our study demonstrate that the glycosyltransferase enzyme contributes to the heterogeneity of intracellular membrane proteins, particularly proteins controlling ER membrane morphologies in response to different cell types and states.
HostingRepository	PRIDE
AnnounceDate	2021-05-10
AnnouncementXML	Submission_2021-05-10_00:27:20.992.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015660
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Didier Vertommen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Phospho; Oxidation; Label:13C(6); Acetyl; Carbamidomethyl
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-01 07:57:29	ID requested
⏵ 1	2021-05-10 00:27:21	announced
2	2021-05-10 22:31:02	announced	2021-05-11: Updated project metadata.

10.1126/SCIADV.ABE8349;

submitter keyword: human, microsomes, glycosylation, Orbitrap, SILAC

Jean-Claude Twizere
contact affiliation	GIGA-Molecular Biology of Diseases-Viral Interactomes Network, Unniversité de Liège, Belgium
contact email	jean-claude.twizere@uliege.be
lab head
Didier Vertommen
contact affiliation	UCL - de Duve Institute, Brussels Belgium
contact email	didier.vertommen@uclouvain.be
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/2021/05/PXD015660

PRIDE project URI

• PRIDE
  1. PXD015660
     1. Label: PRIDE project
     2. Name: Proteome analysis of HeLa cells knocked down for EXT1 expression