Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates

Fredrik Trulsson, Vyacheslav Akimov, Mihaela Robu, Nila Overbeek, David Aureliano Pérez Berrocal, Rashmi G. Shah, Jürgen Cox, Girish M. Shah, Blagoy Blagoev () and Alfred C. O. Vertegaal ()
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Fredrik Trulsson: Cell and Chemical Biology, Leiden University Medical Centre
Vyacheslav Akimov: University of Southern Denmark
Mihaela Robu: Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre
Nila Overbeek: Cell and Chemical Biology, Leiden University Medical Centre
David Aureliano Pérez Berrocal: Cell and Chemical Biology, Leiden University Medical Centre
Rashmi G. Shah: Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre
Jürgen Cox: Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry
Girish M. Shah: Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre
Blagoy Blagoev: University of Southern Denmark
Alfred C. O. Vertegaal: Cell and Chemical Biology, Leiden University Medical Centre

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract The ubiquitin-proteasome axis has been extensively explored at a system-wide level, but the impact of deubiquitinating enzymes (DUBs) on the ubiquitinome remains largely unknown. Here, we compare the contributions of the proteasome and DUBs on the global ubiquitinome, using UbiSite technology, inhibitors and mass spectrometry. We uncover large dynamic ubiquitin signalling networks with substrates and sites preferentially regulated by DUBs or by the proteasome, highlighting the role of DUBs in degradation-independent ubiquitination. DUBs regulate substrates via at least 40,000 unique sites. Regulated networks of ubiquitin substrates are involved in autophagy, apoptosis, genome integrity, telomere integrity, cell cycle progression, mitochondrial function, vesicle transport, signal transduction, transcription, pre-mRNA splicing and many other cellular processes. Moreover, we show that ubiquitin conjugated to SUMO2/3 forms a strong proteasomal degradation signal. Interestingly, PARP1 is hyper-ubiquitinated in response to DUB inhibition, which increases its enzymatic activity. Our study uncovers key regulatory roles of DUBs and provides a resource of endogenous ubiquitination sites to aid the analysis of substrate specific ubiquitin signalling.

Date: 2022
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DOI: 10.1038/s41467-022-30376-7

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