PXD030714

PXD030714 is an original dataset announced via ProteomeXchange.

Title	A ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37
Description	The removal of (poly)ubiquitin (Ub) chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Specific polyubiquitin linkages may lead to distinct cellular effects, with several linkage types associated with proteasomal degradation and others with lysosomal degradation, protein cellular localization or signaling events. Three different deubiquitinating enzymes (DUBs) are associated to the human proteasome, PSMD14/RPN11, USP14 and UCH37/UCHL5. The functional roles and specificities of these proteasomal DUBs remains elusive. To reveal the specificities of these proteasome associated DUBs, we use SILAC based quantitative ubiquitinomics to study the effects of CRISPR-Cas9 based knockout of each of these DUBs on the dynamic cellular ubiquitinome. We report distinct effects on the ubiquitinome and the ability of the proteasome to clear proteins upon removal of either USP14 or UCH37, while the removal of both simultaneously suggests less redundancy for these DUBs than previously anticipated. We also investigated whether the small molecule inhibitor b-AP15 has the potential to specifically target USP14 and UCH37 by comparing treatment in wild-type versus double-knockout cells. Strikingly, we observed broad and severe off-target effects, questioning the alleged specificity of the inhibitor. In conclusion, this work presents novel insights into the function of proteasome associated DUBs and illustrates the power of in-depth ubiquitinomics for screening the activity of DUBs and of DUB modulating compounds.
HostingRepository	PRIDE
AnnounceDate	2022-07-01
AnnouncementXML	Submission_2022-07-01_03:35:53.303.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-04 03:59:23	ID requested
⏵ 1	2022-07-01 03:35:54	announced

van der Wal L, Bezstarosti K, Demmers JAA, A ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37. J Proteomics, 262():104592(2022) [pubmed]

submitter keyword: ubiquitinome, ubiquitinomics, ubiquitin, proteasome, deubiquitinase (DUB), USP14, UCH37/UCHL5, SILAC, quantitative mass spectrometry, parallel reaction monitoring

Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus MC, Rottterdam
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD030714
     1. Label: PRIDE project
     2. Name: A ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37