Abstract
Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Cell |
| Vol/bind | 187 |
| Udgave nummer | 11 |
| Sider (fra-til) | 2875-2892.e21 |
| ISSN | 0092-8674 |
| DOI | |
| Status | Udgivet - 2024 |
Bibliografisk note
Funding Information:We thank members of the Choudhary laboratory for their helpful discussions. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement: 648039) and from the Danish Council for Independent Research (2034-00429B). G.P. is supported by the Novo Nordisk Foundation (grant agreement: NNF17CC0026748). We thank the Big Data Management and Mass Spectrometry Platforms at CPR for their excellent support. The Novo Nordisk Foundation Center for Protein Research is supported financially by the Novo Nordisk Foundation (grant agreement: NNF14CC0001). B.T.W. and S.S. developed the method for quantifying ubiquitylation occupancy. G.P. performed most of the experimental work and analyzed the data. T.N. helped G.P. in the calculation of ubiquitylation occupancy. C.C. and G.P. wrote the manuscript, with input from all authors. C.C. conceived and supervised the project. The authors declare no conflict of interest. During the preparation of this work, the authors used ChatGPT3.5 to check for grammatical errors in the text. After using this tool/service, the authors reviewed and edited the content as needed and take full responsibility for the content of the publication.
Funding Information:
We thank members of the Choudhary laboratory for their helpful discussions. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement: 648039 ) and from the Danish Council for Independent Research ( 2034-00429B ). G.P. is supported by the Novo Nordisk Foundation (grant agreement: NNF17CC0026748 ). We thank the Big Data Management and Mass Spectrometry Platforms at CPR for their excellent support. The Novo Nordisk Foundation Center for Protein Research is supported financially by the Novo Nordisk Foundation (grant agreement: NNF14CC0001 ).
Publisher Copyright:
© 2024 The Authors