ArticleCell chemical biology2021
Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity.
Article in Cell chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
- Unveiling muscle fatigue: identifying key gene biomarkers and therapeutic targets.Molecular and cellular biochemistry · 2026Article
- Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis.Angewandte Chemie (International ed. in English) · 2025Article
- CARM1-mediated OGT arginine methylation promotes non-small cell lung cancer glycolysis by stabilizing OGT.Cell death & disease · 2024Article
- Specificity profiling of deubiquitylases against endogenously generated ubiquitin-protein conjugates.Cell chemical biology · 2024Article
- Potential roles of UCH family deubiquitinases in tumorigenesis and chemical inhibitors developed against them.American journal of cancer research · 2024Review
- Identification of Deubiquitinase Substrates in Xenopus Egg Extract.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.Genomics, proteomics & bioinformatics · 2022Article
- FeJournal of proteomics · 2022Article
- Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates.Nature communications · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
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 used quantitative mass spectrometry to identify proteins whose ubiquitylation or stability is altered by broad DUB inhibition, and confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this 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 substrates. We found that USP7 has a unique ability to broadly antagonize degradation. Together, we present an approach to identify DUB substrates and characterize DUB specificity that overcomes challenges posed by DUB redundancy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.