PXD003936-1

PXD003936 is an original dataset announced via ProteomeXchange.

Title	A proteomic survey defines proteasome-dependent and independent VCP substrates in human cells
Description	Valosin-containing protein (VCP) is an evolutionary conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome and autophagy-lysosome pathway. Despite the central role of VCP in the regulation of protein homeostasis, the identity and nature of its cellular substrates remains poorly defined. Here, we employed chemical inhibition of VCP and quantitative ubiquitin remnant profiling to reveal the substrate spectrum of VCP in human cells. We demonstrate that inhibition of VCP globally perturbs cellular ubiquitylation and increases the ubiquitylation of a distinct set of proteins compared to proteasome inhibition. We discover ~450 substrates of VCP residing in different cellular compartments, many of which are chromatin-associated, and demonstrate widespread proteasome-independent functions of VCP. Moreover, we show that VCP mediates the degradation of the transcription factor c-Myc and thereby regulates its activity. In summary, our study identifies proteasome-dependent and independent substrates of VCP, and serves as a resource for further functional investigations of VCP and its substrates in different cellular processes.
HostingRepository	PRIDE
AnnounceDate	2018-02-09
AnnouncementXML	Submission_2018-02-09_11:29:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Beli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-10 23:54:48	ID requested
⏵ 1	2018-02-09 11:29:37	announced
2	2018-02-14 02:01:01	announced	Updated project metadata.
3	2019-02-12 08:07:14	announced	Updated project metadata.
4	2024-10-22 04:04:52	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Protein homeostasis, quantitative mass spectrometry, ubiquitin-proteasome system, ubiquitin remnant profiling, VCP

Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
lab head
Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
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/2018/02/PXD003936

PRIDE project URI

• PRIDE
  1. PXD003936
     1. Label: PRIDE project
     2. Name: A proteomic survey defines proteasome-dependent and independent VCP substrates in human cells