PXD022762

PXD022762 is an original dataset announced via ProteomeXchange.

Title	Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity
Description	Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs can act on the same substrate, thwarting genetic approaches. Here, we circumvent redundancy by chemically inhibiting multiple DUBs simultaneously in Xenopus egg extract. We discovered a set of proteins that depends on DUBs for their stability and we confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this approach, developing a new method to profile DUB specificity. By adding recombinant DUBs to extract where DUB activity was broadly inhibited, but ubiquitylation and degradation were active at physiological rates, we profiled the ability of DUBs to rescue degradation of these new substrates. We found that USP7 has a unique ability to broadly antagonize their degradation. Together, we identify novel DUB substrates and present an approach to characterize DUB specificity that overcomes challenges posed by DUB redundancy.
HostingRepository	PRIDE
AnnounceDate	2022-09-02
AnnouncementXML	Submission_2022-09-02_12:01:22.242.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	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-26 03:17:15	ID requested
⏵ 1	2022-09-02 12:01:23	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: Xenopus, SPS-MS3, ubiquitin, dub

Joao A. Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.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. PXD022762
     1. Label: PRIDE project
     2. Name: Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity