Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates

Nature Communications, vol. 13, pp. 2736

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.

Authors 10

1. Fredrik Trulsson Aachen Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands

2. Vyacheslav Akimov

   University of Southern Denmark

   Affiliation as printed

   Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

3. Mihaela Robu

   Université Laval · Centre de recherche du CHU de Québec-Université Laval

   Affiliation as printed

   Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada

4. Nila K. van Overbeek Aachen Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands

5. David A. Pérez Berrocal Aachen Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands

6. Rashmi G. Shah

   Université Laval · Centre de recherche du CHU de Québec-Université Laval

   Affiliation as printed

   Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada

7. Jürgen Cox

   Max Planck Institute of Biochemistry

   Affiliation as printed

   Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany

8. Girish M. Shah

   Université Laval · Centre de recherche du CHU de Québec-Université Laval

   Affiliation as printed

   Laboratory for Skin Cancer Research, CHU de Québec Laval University Hospital Research Centre, Québec, QC, Canada

9. Blagoy Blagoev corresponding

   University of Southern Denmark

   Affiliation as printed

   Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. bab@bmb.sdu.dk

   Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

10. Alfred C.O. Vertegaal corresponding Aachen Cell and Chemical Biology

    Leiden University · Leiden University Medical Center

    Affiliation as printed

    Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands. vertegaal@lumc.nl

    Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands