PXD030644

PXD030644 is an original dataset announced via ProteomeXchange.

Title	Deubiquitinating enzymes and the proteasome regulate unique sets of ubiquitin substrates.
Description	The ubiquitin-proteasome axis has been extensively explored at a system-wide level, but the impact of deubiquitinating enzymes (DUBs) on the ubiquitinome remains largely unknown. Using UbiSite technology and inhibitors, we have compared the contributions of the proteasome and DUBs on the ubiquitinome. We uncovered large differential dynamic Ub signalling networks with substrates and sites uniquely regulated by DUBs or by the proteasome, highlighting the role of DUBs in degradation-independent ubiquitin signalling. DUBs regulate substrates via nearly 40,000 unique sites. Moreover, we found that ubiquitin conjugated to SUMO2/3 forms a unidirectional proteasomal degradation signal with strikingly rapid kinetics compared to ubiquitin polymers only. We found that PARP1, is hyper ubiquitinated in response to DUB inhibition, increasing its enzymatic activity. Our findings highlight the key regulatory roles of DUBs on ubiquitin dynamics.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:36:42.667.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vyacheslav Akimov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-24 16:21:44	ID requested
1	2022-05-23 04:38:06	announced
⏵ 2	2024-10-22 05:36:50	announced	2024-10-22: Updated project metadata.

10.1038/s41467-022-30376-7;

Trulsson F, Akimov V, Robu M, van Overbeek N, Berrocal DAP, Shah RG, Cox J, Shah GM, Blagoev B, Vertegaal ACO, Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates. Nat Commun, 13(1):2736(2022) [pubmed]

submitter keyword: DIA,The ubiquitin-proteasome system, LC-MS/MS

Dr. Prof. Blagoy Blagoev
contact affiliation	Department of Biochemistry and Molecular Biology, University of Southern Denmark
contact email	bab@bmb.sdu.dk
lab head
Vyacheslav Akimov
contact affiliation	Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
contact email	akimov@bmb.sdu.dk
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/2022/05/PXD030644

PRIDE project URI

• PRIDE
  1. PXD030644
     1. Label: PRIDE project
     2. Name: Deubiquitinating enzymes and the proteasome regulate unique sets of ubiquitin substrates.