Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code

Abstract

Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.

Keywords: DUBs; acetylation; hydroxylation; oxidation; phosphorylation; post-translational modifications; sumoylation; ubiquitination.

FIGURE 1

PTMs mediated ubiquitination and deubiquitination process. Protein Ubiquitination is a cascade reaction catalysed by E1 activating, E2 conjugating and E3 ligating enzymes. This can lead to the formation of distinct types of ubiquitin modifications, all of which can be reversed by deubiquitylating enzymes (DUBs). DUBs are regulated strictly by various post translational modifications (PTMs), including phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation and hydroxylation. Numbers in brackets indicate the number of enzymes in each family.

FIGURE 2

Localization and PTMs induced translocation of DUBs. (A) DUBs have been reported to localize and function in almost every intracellular compartment, such as nucleolus, cell membrane and mitochrondria etc., and have specific roles. Importantly, the function of DUB can be expanded by ensuring that a single DUB localizes to distinct organelles as shown, for example, for JosD1, USP4 and USP25 etc. (B) PTMs, such as phosphorylation and ubiquitination, play an important role in regulation the alternative localization of DUB. For example, phosphorylation of BAP1, USP4 and USP8 causes them to relocate from the nucleus to the cytosol. In contrast, phosphorylation of OTUB1, Ataxin3, USP15, USP10, and USP1 triggers its translocation from cytosol to the nucleus. Additionally, ubiquitination of JosD1 leads its translocation from cytosol to cell membrane. The figure was generated based on the reported studies.

FIGURE 3

PTMs induced activity changes of DUBs. (A) Complex crosstalks of different PTMs often occur on DUBs with different effects. For example, USP25 can be modified by phosphorylation, SUMOylation and ubiquitination, which affect the activity and stability of USP25. (B) Many DUBs undergo one or more PTMs, such as USP13 can be phosphorylated at Ser114, Thr196, Tyr708, leading to different biological events. (C) and (D) DUB activities can also be changed by PTMs such as phosphorylation, ubiquitylation, and SUMOylation. The arrow below shows the change in DUBs’ enzyme activity after PTMs modification.

FIGURE 4

Structure and model of PTMs-induced conformation changes of DUBs. (A). Phosphorylation induced conformation changes of OTUD5 after Ub binding. (B). Phosphorylation induced direct conformation changes of USP14 (C). Phosphorylation induced partner binding of USP8. (D). Model of PTMs induced conformation changes of DUBs. (a). phosphorylation-induced conformation changes (b). phosphorylation-induced allosterically regulated conformation changes (c). phosphorylation-induced substrate (d) or protein partner (e) binding and conformation changes.