PXD016164

PXD016164 is an original dataset announced via ProteomeXchange.

Title	Unmasking functional redundancy of deubiquitylases enables specificity profiling and discovery of novel proteasome substrates
Description	Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control the stability or activity of their substrates. Identifying DUB substrates is challenging and genetic approaches can be thwarted by redundant action of DUBs. Here, we circumvented redundancy by broadly inhibiting DUBs in Xenopus egg extract and used quantitative mass spectrometry to identify over thirty proteins that undergo proteasomal degradation, the majority of which have not been reported as DUB substrates. These results were confirmed with recombinant human proteins, demonstrating the conservation of their DUB-dependent stability. We used these substrates to profile the ability of a panel of DUBs to rescue degradation. This approach revealed that USP7, uniquely among the 14 DUBs tested, has a broad ability to rescue degradation. USP21, which is used widely to nonspecifically deubiquitylate proteins in vitro, was unable to rescue degradation, highlighting the importance of profiling enzyme activity in a physiological system. Together, we identify new DUB substrates and present a system to characterize physiological DUB specificity, overcoming the challenges posed by DUB redundancy.
HostingRepository	PRIDE
AnnounceDate	2022-09-02
AnnouncementXML	Submission_2022-09-02_12:46:50.006.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; ubiquitinylated lysine; deaminated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-06 02:05:41	ID requested
⏵ 1	2022-09-02 12:46:50	announced

Rossio V, Paulo JA, Chick J, Brasher B, Gygi SP, King RW, Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity. Cell Chem Biol, 28(4):487-502.e5(2021) [pubmed]

submitter keyword: Ubiquitin, TMT, Xenopus, DUB, degradation, proteasome

Joao A. Paulo
contact affiliation	Harvard Medical School Boston, MA 02115, USA
contact email	Joao_Paulo@hms.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016164
     1. Label: PRIDE project
     2. Name: Unmasking functional redundancy of deubiquitylases enables specificity profiling and discovery of novel proteasome substrates