Cell Chem Biol 2024 Jul 18;317:1349-1362.e5. doi: 10.1016/j.chembiol.2024.05.001.

Specificity profiling of deubiquitylases against endogenously generated ubiquitin-protein conjugates.

Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high-impact DUBs (USP7, USP9X, USP36, USP15, and USP24) that each reduced ubiquitylation of over 10% of the isolated proteins. Candidate substrates of high-impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.

PubMed ID: 38810651
PMC ID: PMC11260241
Article link: Cell Chem Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: alg13 atxn3 bap1 birc6 calcoco2 cyld eps15 hectd1 josd1 josd2 mindy1 mindy2 mindy3 mindy4 mindy4b optn otub1 otub2 otud1 otud3 otud4 otud5 otud6b otud7a otud7b otulin otulinl phb1 phb2 tollip tom1 trafd1 uchl1 uchl3 uchl5 usp1 usp10 usp12 usp13 usp14 usp15 usp16 usp18 usp19 usp2 usp20 usp21 usp22 usp24 usp25 usp28 usp3 usp30 usp31 usp32 usp33 usp34 usp35 usp36 usp37 usp38 usp39 usp4 usp40 usp42 usp43 usp44 usp45 usp47 usp48 usp49 usp5 usp53 usp54 usp7 usp8 usp9x vcpip1 yod1 zranb1 zup1
GO keywords: deubiquitinase activator activity