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From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization

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From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization cells Review From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization Yamen Abu Ahmad † , Avital Oknin-Vaisman † , Eliya Bitman-Lotan † and Amir Orian * Rappaport Faculty of Medicine, R-TICC, Technion-IIT, Efron St. Bat-Galim, Haifa 3109610, Israel; [email protected] (Y.A.A.); [email protected] (A.O.-V.); [email protected] (E.B.-L.) * Correspondence: [email protected]; Tel.: +972-547558047 † These authors contributed to this work equally. Abstract: A hallmark of cancer is dysregulated protein turnover (proteostasis), which involves pathologic ubiquitin-dependent degradation of tumor suppressor proteins, as well as increased oncoprotein stabilization. The latter is due, in part, to mutation within sequences, termed degrons, which are required for oncoprotein recognition by the substrate-recognition enzyme, E3 ubiquitin ligase. Stabilization may also result from the inactivation of the enzymatic machinery that mediates the degradation of oncoproteins. Importantly, inactivation in cancer of E3 enzymes that regulates the physiological degradation of oncoproteins, results in tumor cells that accumulate multiple active oncoproteins with prolonged half-lives, leading to the development of “degradation-resistant” cancer cells. In addition, specific sequences may enable ubiquitinated proteins to evade degradation at the 26S proteasome. While the ubiquitin-proteasome pathway was originally discovered as central for protein degradation, in cancer cells a ubiquitin-dependent protein stabilization pathway actively translates transient mitogenic signals into long-lasting protein stabilization and enhances the activity of key oncoproteins. A central enzyme in this pathway is the ubiquitin ligase RNF4. An intimate Citation: Abu Ahmad, Y.; Oknin-Vaisman, A.; Bitman-Lotan, E.; link connects protein stabilization with tumorigenesis in experimental models as well as in the clinic, Orian, A. From the Evasion of suggesting that pharmacological inhibition of protein stabilization has potential for personalized Degradation to Ubiquitin-Dependent medicine in cancer. In this review, we highlight old observations and recent advances in our Protein Stabilization. Cells 2021, 10, knowledge regarding protein stabilization. 2374. https://doi.org/10.3390/ cells10092374 Keywords: ubiquitin; proteasome; degron; heterotypic-Ub chains; E3 ubiquitin ligases; degradation; protein-stabilization; degradation-resistant tumors; RNF4; STUbL; oncoproteins; cancer Academic Editor: Francois-Michel Boisvert Received: 11 August 2021 1. Overview Accepted: 4 September 2021 Published: 9 September 2021 The dynamic stability of proteins, which is a fundamental concept in biology, was discovered by Rudolph Schonheimer [1]. It is, however, well known that proteomes exhibit Publisher’s Note: MDPI stays neutral a wide range of protein half-lives [2]. While some intracellular proteins are extremely with regard to jurisdictional claims in long-lived (LLPs; [3]), many regulatory proteins degrade rapidly, exhibiting a half-life of published maps and institutional affil- only minutes. In this study, we relate to protein abundance/stabilization and to changes in iations. protein half-life that are determined by regulated degradation rather than by the biophys- ical structural properties of the protein. A central system that mediates ATP-dependent degradation of proteins is the ubiquitin-proteasome system (UPS; [4–6]). The degradation rate of a given protein is not, however, fixed; it is physiologically dynamic and dramatically affected by post-translational modifications such as phosphorylation, hydroxylation, acety- Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. lation, SUMOylation, and methylation, that may directly effects degrons [7]. For example, κ α This article is an open access article upon immune challenge, signal-induced phosphorylation of the inhibitory protein, I B , distributed under the terms and converts the extremely stable protein into a rapidly degraded phospho-protein, enabling conditions of the Creative Commons immune response [8,9]. Attribution (CC BY) license (https:// Protein stability depends on intrinsic structures within the targeted proteins, called creativecommons.org/licenses/by/ degrons, as well as on enzymes that mediate the ubiquitination of the protein substrate. 4.0/). A recent systemic analysis of primary tumors established that stabilizing mutations in Cells 2021, 10, 2374. https://doi.org/10.3390/cells10092374 https://www.mdpi.com/journal/cells CellsCells2021 2021, 10, ,10 2374, x FOR PEER REVIEW 2 of2 17 of 16 degronsA recent and systemic inactivating analysis mutations of primary in ubiquitin tumors established ligases (E3), that which stabilizing mediate mutation the recognitions in ofdegrons such degrons, and inactivating are driving mutations events in tumorigenesisubiquitin ligases [10 (E3),]. Active which stabilization, mediate the recogni- or limited proteolysis,tion of such also degrons, depends are driving on the type events of ubiquitinin tumorigenesis chains catalyzed [10]. Active on stabilization, the protein substrates. or lim- Inited addition, proteolysis, a ubiquitin-dependent also depends on proteinthe type stabilization of ubiquitin pathway chains catalyzed actively stabilizes on the protein proteins insubstrates. cancer. This In addition, pathway isa ubiquitin-dependent situated upstream to protein and independent stabilization of thepathway machinery actively involved sta- inbilizes their proteins degradation. in cancer. A central This pathway enzyme inis thissituated pathway upstream is the to ubiquitin and independent ligase RNF4 of the [11 ]. Inmachinery this review, involved we address in their several degradation. aspects A of cent proteinral enzyme stabilization. in this First,pathway we discussis the ubiqui- cases of proteintin ligase stabilization RNF4 [11]. that In this result review, from we mutations address in several degrons aspects or inactivation of protein ofstabilization. the enzymes thatFirst, mediate we discuss the cases degradation of protein of stabilization these proteins. that Second,result from we mutati focusons on casesin degrons of protein or stabilizationinactivation of that the stem enzymes from that active mediate ubiquitin-dependent the degradation of protein these proteins. stabilization, Second, which we is highlyfocus on relevant cases of to protein cancer (Figurestabilization1). that stem from active ubiquitin-dependent protein stabilization, which is highly relevant to cancer (Figure 1). FigureFigure 1. 1.Mechanisms Mechanisms of of protein protein stabilization. stabilization. Schematic Schematic diagram diagram for for mechanisms mechanisms resulting resulting in in protein protein stabilization stabilization that that are are discussed in this review, see text for details. discussed in this review, see text for details. 2. Evading Recognition I: Protein Stabilization Due to Lacking or Mutated Degrada- 2. Evading Recognition I: Protein Stabilization Due to Lacking or Mutated Degradationtion Signals Signals DegronsDegrons areare shortshort amino-acid sequences sequences that that determine determine the the stability stability of ofproteins. proteins. They They areare divided divided accordingaccording to their position position on on th thee protein protein substrate substrate to to N-terminal, N-terminal, C-terminal, C-terminal, andand internalinternal degrons.degrons. The biochemical nature nature of of the the N- N- and and C-terminal C-terminal degrons degrons and and the the enzymaticenzymatic pathways pathways dedicateddedicated to the the recognitio recognitionn thereof thereof are are discussed discussed in in detail detail in ina recent a recent reviewreview by by Varshavsky Varshavsky [12 [12],], who who also also discovered discovered the the contribution contribution ofof N-terminalN-terminal degronsdegrons to proteinto protein stability stability in 1986in 1986 [13 [13].]. InternalInternal degronsdegrons serve as recognition recognition motifs motifs for for the the diverse diverse group group of of E3 E3 ubiquitin ubiquitin ligasesligases [[14].14]. Internal Internal degrons degrons were were initially initially thought thought to mediate to mediate only the only docking the docking and phys- and physicalical interaction interaction between between the substrate the substrate and the and E3 theubiquitin E3 ubiquitin ligases ligasesthat catalyze that catalyze their ubiq- their ubiquitinationuitination and andsubsequent subsequent degra degradation.dation. However, However, it is now it is clear now that clear these that motifs these motifsalso contain sequences that enable stabilizing signals [15–17]. Among the first degrons to be also contain sequences that enable stabilizing signals [15–17]. Among the first degrons to identified was the Delta motif, a stretch of 27 amino acids that is present in the c-Jun proto- be identified was the Delta motif, a stretch of 27 amino acids that is present in the c-Jun oncogene and is required for its ubiquitin-dependent degradation. This motif is not pre- proto-oncogene and is required for its ubiquitin-dependent degradation. This motif is not sent in v-Jun, the oncogenic viral protein, or in its closely related JunD, which exhibits a present in v-Jun, the oncogenic viral protein, or in its closely related JunD, which exhibits a longer half-life [18,19]. longer half-life [18,19]. Another example of a short recognition motif is a motif present in P53 tumor sup- Another example
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