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Furukawa, Manabu, Yanping Zhang, Joseph McCarville, Tomohiko Ohta, and Yue Xiong. "The CUL1 C-Terminal Sequence and ROC1 Are Required for Efficient Nuclear Accumulation, NEDD8 Modification, and Ubiquitin Ligase Activity of CUL1." Molecular and Cellular Biology 20, no. 21 (November 1, 2000): 8185–97. http://dx.doi.org/10.1128/mcb.20.21.8185-8197.2000.
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ABSTRACT Members of the cullin and RING finger ROC protein families form heterodimeric complexes to constitute a potentially large number of distinct E3 ubiquitin ligases. We report here that the highly conserved C-terminal sequence in CUL1 is dually required, both for nuclear localization and for modification by NEDD8. Disruption of ROC1 binding impaired nuclear accumulation of CUL1 and decreased NEDD8 modification in vivo but had no effect on NEDD8 modification of CUL1 in vitro, suggesting that ROC1 promotes CUL1 nuclear accumulation to facilitate its NEDD8 modification. Disruption of NEDD8 binding had no effect on ROC1 binding, nor did it affect nuclear localization of CUL1, suggesting that nuclear localization and NEDD8 modification of CUL1 are two separable steps, with nuclear import preceding and required for NEDD8 modification. Disrupting NEDD8 modification diminishes the IκBα ubiquitin ligase activity of CUL1. These results identify a pathway for regulation of CUL1 activity—ROC1 and the CUL1 C-terminal sequence collaboratively mediate nuclear accumulation and NEDD8 modification, facilitating assembly of active CUL1 ubiquitin ligase. This pathway may be commonly utilized for the assembly of other cullin ligases.
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Baek, Kheewoong, Daniel C. Scott, and Brenda A. Schulman. "NEDD8 and ubiquitin ligation by cullin-RING E3 ligases." Current Opinion in Structural Biology 67 (April 2021): 101–9. http://dx.doi.org/10.1016/j.sbi.2020.10.007.
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Kamada, Shinji. "Inhibitor of apoptosis proteins as E3 ligases for ubiquitin and NEDD8." BioMolecular Concepts 4, no. 2 (April 1, 2013): 161–71. http://dx.doi.org/10.1515/bmc-2012-0036.
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AbstractThe inhibitors of apoptosis proteins (IAPs) are endogenous inhibitors for apoptosis. Apoptosis is carried out by caspases, which are the family of cystein proteases. IAPs regulate caspases through two conserved regions, the baculovirus IAP repeats (BIRs) and the really interesting new gene (RING) domains. Although the BIRs are responsible for binding to caspases, the RING domain can act as a ubiquitin-E3 ligase, leading to ubiquitylation of IAPs themselves and their pro-apoptotic IAP counterparts such as caspases. Recently, it is reported that another ubiquitin-like protein, neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8), is also involved in the regulation of apoptosis through neddylation of caspases mediated by IAPs. On the contrary, the results against the function of IAPs as a NEDD8-E3 ligase are also suggested. This review presents the summary of IAPs, caspases, and the ubiquitin-proteasome system and how their interactions influence the regulation of apoptosis.
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Benjamin, Sigi, and Hermann Steller. "Another Tier for Caspase Regulation: IAPs as NEDD8 E3 Ligases." Developmental Cell 19, no. 6 (December 2010): 791–92. http://dx.doi.org/10.1016/j.devcel.2010.11.014.
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Keuss, Matthew J., Yann Thomas, Robin Mcarthur, Nicola T. Wood, Axel Knebel, and Thimo Kurz. "Characterization of the mammalian family of DCN-type NEDD8 E3 ligases." Journal of Cell Science 129, no. 7 (February 18, 2016): 1441–54. http://dx.doi.org/10.1242/jcs.181784.
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Broemer, Meike, Tencho Tenev, Kristoffer T. G. Rigbolt, Sophie Hempel, Blagoy Blagoev, John Silke, Mark Ditzel, and Pascal Meier. "Systematic In Vivo RNAi Analysis Identifies IAPs as NEDD8-E3 Ligases." Molecular Cell 40, no. 5 (December 2010): 810–22. http://dx.doi.org/10.1016/j.molcel.2010.11.011.
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Hjerpe, Roland, Yann Thomas, Jesse Chen, Aleksandra Zemla, Siobhan Curran, Natalia Shpiro, Lawrence R. Dick, and Thimo Kurz. "Changes in the ratio of free NEDD8 to ubiquitin triggers NEDDylation by ubiquitin enzymes." Biochemical Journal 441, no. 3 (January 16, 2012): 927–39. http://dx.doi.org/10.1042/bj20111671.
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Ubiquitin and UBL (ubiquitin-like) modifiers are small proteins that covalently modify other proteins to alter their properties or behaviours. Ubiquitin modification (ubiquitylation) targets many substrates, often leading to their proteasomal degradation. NEDD8 (neural-precursor-cell-expressed developmentally down-regulated 8) is the UBL most closely related to ubiquitin, and its best-studied role is the activation of CRLs (cullin-RING ubiquitin ligases) by its conjugation to a conserved C-terminal lysine residue on cullin proteins. The attachment of UBLs requires three UBL-specific enzymes, termed E1, E2 and E3, which are usually well insulated from parallel UBL pathways. In the present study, we report a new mode of NEDD8 conjugation (NEDDylation) whereby the UBL NEDD8 is linked to proteins by ubiquitin enzymes in vivo. We found that this atypical NEDDylation is independent of classical NEDD8 enzymes, conserved from yeast to mammals, and triggered by an increase in the NEDD8 to ubiquitin ratio. In cells, NEDD8 overexpression leads to this type of NEDDylation by increasing the concentration of NEDD8, whereas proteasome inhibition has the same effect by depleting free ubiquitin. We show that bortezomib, a proteasome inhibitor used in cancer therapy, triggers atypical NEDDylation in tissue culture, which suggests that a similar process may occur in patients receiving this treatment.
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Zhou, Lihong, and Felicity Z. Watts. "Nep1, a Schizosaccharomyces pombe deneddylating enzyme." Biochemical Journal 389, no. 2 (July 5, 2005): 307–14. http://dx.doi.org/10.1042/bj20041991.
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Nedd8 is a ubiquitin-like modifier that is attached to the cullin components of E3 ubiquitin ligases. More recently, p53 has also been shown to be Nedd8-modified. Nedd8 attachment occurs in a manner similar to that observed for other ubiquitin-like modifiers. In the present study, we report on the characterization of Nep1, a deneddylating enzyme in fission yeast (Schizosaccharomyces pombe). Unlike loss of ned8, deletion of the nep1 gene is not lethal, although nep1.d cells are heterogeneous in length, suggesting a defect in cell-cycle progression. Viability of nep1.d cells is dependent on a functional spindle checkpoint but not on the DNA integrity checkpoint. Deletion of a related gene (nep2), either alone or in combination with nep1.d, also has little effect on cell viability. We show that Nep1 can deneddylate the Pcu1, Pcu3 and Pcu4 cullins in vitro and that its activity is sensitive to N-ethylmaleimide, consistent with the idea that it is a member of the cysteine protease family. nep1.d cells accumulate Nedd8-modified proteins, although these do not correspond to modified forms of the cullins, suggesting that, although Nep1 can deneddylate cullins in vitro, this is not its main function in vivo. Nep1 can be co-precipitated with the signalosome subunit Csn5. Nep1 itself is present in a high-molecular-mass complex, but the presence of this complex is not dependent on the production of intact signalosomes. Our results suggest that, in vivo, Nep1 may be responsible for deneddylating proteins other than cullins.
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Adhvaryu, Keyur K., Jordan D. Gessaman, Shinji Honda, Zachary A. Lewis, Paula L. Grisafi, and Eric U. Selker. "The Cullin-4 Complex DCDC Does Not Require E3 Ubiquitin Ligase Elements To Control Heterochromatin in Neurospora crassa." Eukaryotic Cell 14, no. 1 (October 31, 2014): 25–28. http://dx.doi.org/10.1128/ec.00212-14.
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ABSTRACT The cullin-4 (CUL4) complex DCDC ( D IM-5/-7/-9/ C UL4/ D DB1 c omplex) is essential for DNA methylation and heterochromatin formation in Neurospora crassa . Cullins form the scaffold of cullin-RING E3 ubiquitin ligases (CRLs) and are modified by the covalent attachment of NEDD8, a ubiquitin-like protein that regulates the stability and activity of CRLs. We report that neddylation is not required for CUL4-dependent DNA methylation or heterochromatin formation but is required for the DNA repair functions. Moreover, the RING domain protein RBX1 and a segment of the CUL4 C terminus that normally interacts with RBX1, the E2 ligase, CAND1, and CSN are dispensable for DNA methylation and heterochromatin formation by DCDC. Our study provides evidence for the noncanonical functions of core CRL components.
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Onel, Melis, Fidan Sumbul, Jin Liu, Ruth Nussinov, and Turkan Haliloglu. "Cullin neddylation may allosterically tune polyubiquitin chain length and topology." Biochemical Journal 474, no. 5 (February 20, 2017): 781–95. http://dx.doi.org/10.1042/bcj20160748.
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Conjugation of Nedd8 (neddylation) to Cullins (Cul) in Cul-RING E3 ligases (CRLs) stimulates ubiquitination and polyubiquitination of protein substrates. CRL is made up of two Cul-flanked arms: one consists of the substrate-binding and adaptor proteins and the other consists of E2 and Ring-box protein (Rbx). Polyubiquitin chain length and topology determine the substrate fate. Here, we ask how polyubiquitin chains are accommodated in the limited space available between the two arms and what determines the polyubiquitin linkage topology. We focus on Cul5 and Rbx1 in three states: before Cul5 neddylation (closed state), after neddylation (open state), and after deneddylation, exploiting molecular dynamics simulations and the Gaussian Network Model. We observe that regulation of substrate ubiquitination and polyubiquitination takes place through Rbx1 rotations, which are controlled by Nedd8–Rbx1 allosteric communication. Allosteric propagation proceeds from Nedd8 via Cul5 dynamic hinges and hydrogen bonds between the C-terminal domain of Cul5 (Cul5CTD) and Rbx1 (Cul5CTD residues R538/R569 and Rbx1 residue E67, or Cul5CTD E474/E478/N491 and Rbx1 K105). Importantly, at each ubiquitination step (homogeneous or heterogeneous, linear or branched), the polyubiquitin linkages fit into the distances between the two arms, and these match the inherent CRL conformational tendencies. Hinge sites may constitute drug targets.
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Chang, Fang-Mei, Sara M. Reyna, Jose C. Granados, Sung-Jen Wei, Wendy Innis-Whitehouse, Shivani K. Maffi, Edward Rodriguez, Thomas J. Slaga, and John D. Short. "Inhibition of Neddylation Represses Lipopolysaccharide-induced Proinflammatory Cytokine Production in Macrophage Cells." Journal of Biological Chemistry 287, no. 42 (August 27, 2012): 35756–67. http://dx.doi.org/10.1074/jbc.m112.397703.
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Cullin-RING E3 ligases (CRLs) are a class of ubiquitin ligases that control the proteasomal degradation of numerous target proteins, including IκB, and the activity of these CRLs are positively regulated by conjugation of a Nedd8 polypeptide onto Cullin proteins in a process called neddylation. CRL-mediated degradation of IκB, which normally interacts with and retains NF-κB in the cytoplasm, permits nuclear translocation and transactivation of the NF-κB transcription factor. Neddylation occurs through a multistep enzymatic process involving Nedd8 activating enzymes, and recent studies have shown that the pharmacological agent, MLN4924, can potently inhibit Nedd8 activating enzymes, thereby preventing neddylation of Cullin proteins and preventing the degradation of CRL target proteins. In macrophages, regulation of NF-κB signaling functions as a primary pathway by which infectious agents such as lipopolysaccharides (LPSs) cause the up-regulation of proinflammatory cytokines. Here we have analyzed the effects of MLN4924, and compared the effects of MLN4924 with a known anti-inflammatory agent (dexamethasone), on certain proinflammatory cytokines (TNF-α and IL-6) and the NF-κB signaling pathway in LPS-stimulated macrophages. We also used siRNA to block neddylation to assess the role of this molecular process during LPS-induced cytokine responsiveness. Our results demonstrate that blocking neddylation, either pharmacologically or using siRNA, abrogates the increase in certain proinflammatory cytokines secreted from macrophages in response to LPS. In addition, we have shown that MLN4924 and dexamethasone inhibit LPS-induced cytokine up-regulation at the transcriptional level, albeit through different molecular mechanisms. Thus, neddylation represents a novel molecular process in macrophages that can be targeted to prevent and/or treat the LPS-induced up-regulation of proinflammatory cytokines and the disease processes associated with their up-regulation.
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Choo, Yin Yin, Boon Kim Boh, Jessica Jie Wei Lou, Jolane Eng, Yee Chin Leck, Benjamin Anders, Peter G. Smith, and Thilo Hagen. "Characterization of the role of COP9 signalosome in regulating cullin E3 ubiquitin ligase activity." Molecular Biology of the Cell 22, no. 24 (December 15, 2011): 4706–15. http://dx.doi.org/10.1091/mbc.e11-03-0251.
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Cullin RING ligases (CRLs) are the largest family of cellular E3 ubiquitin ligases and mediate polyubiquitination of a number of cellular substrates. CRLs are activated via the covalent modification of the cullin protein with the ubiquitin-like protein Nedd8. This results in a conformational change in the cullin carboxy terminus that facilitates the ubiquitin transfer onto the substrate. COP9 signalosome (CSN)-mediated cullin deneddylation is essential for CRL activity in vivo. However, the mechanism through which CSN promotes CRL activity in vivo is currently unclear. In this paper, we provide evidence that cullin deneddylation is not intrinsically coupled to substrate polyubiquitination as part of the CRL activation cycle. Furthermore, inhibiting substrate-receptor autoubiquitination is unlikely to account for the major mechanism through which CSN regulates CRL activity. CSN also did not affect recruitment of the substrate-receptor SPOP to Cul3, suggesting it may not function to facilitate the exchange of Cul3 substrate receptors. Our results indicate that CSN binds preferentially to CRLs in the neddylation-induced, active conformation. Binding of the CSN complex to active CRLs may recruit CSN-associated proteins important for CRL regulation. The deneddylating activity of CSN would subsequently promote its own dissociation to allow progression through the CRL activation cycle.
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Swords, Ronan T., Kevin R. Kelly, Peter G. Smith, James J. Gansey, Devalingam Mahalingam, Swaminathan Padmanabhan, Michael C. O'Dwyer, Steffan T. Nawrocki, Francis J. Giles, and Jennifer S. Carew. "MLN4924, A Novel First in Class Small Molecule Inhibitor of the Nedd8 Activating Enzyme (NAE), Has Potent Activity in Preclinical Models of Acute Myeloid Leukemia." Blood 114, no. 22 (November 20, 2009): 1021. http://dx.doi.org/10.1182/blood.v114.22.1021.1021.
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Abstract Abstract 1021 Poster Board I-43 The coordinated balance between the synthesis and degradation of proteins is an important regulator of cancer cell biology. The ubiquitin-proteasome system (UPS) is responsible for the timed destruction of many proteins including key mediators of fundamental signaling cascades and critical regulators of cell cycle progression and transcription. Within the UPS, the E3 ligases are multi-protein complexes whose specificity is established by their individual components as well as post-translational modifications by various factors including the ubiquitin-like molecule, Nedd8. The Nedd8 activating enzyme (NAE) has been identified as an essential regulator of the Nedd8 conjugation pathway, which controls the activity of the cullin-dependent E3 ubiquitin ligases. The cullins direct the ubiquitination and subsequent degradation of many proteins with important roles in cell cycle progression (p27, cyclin E), DNA damage (Cdt-1), stress response (NRF-2, HIF1α) and signal transduction (IκBα). Acute myeloid leukemia (AML) is a disease of the elderly and prognosis is extremely poor with a median overall survival of just 2 months for untreated patients. As such, novel therapeutic strategies are urgently needed to improve clinical outcomes. Considering that Nedd8-mediated control of protein homeostasis is vitally important for the survival of AML cells, we hypothesized that disrupting this process would inhibit proliferation and induce cell death. We tested this hypothesis by investigating the preclinical anti-leukemic activity of MLN4924, a novel first in class small molecule inhibitor of the Nedd8 activating enzyme. MLN4924 induced DNA damage followed by rapid and selective caspase-dependent cell death in AML cell lines and primary AML cells from patients, but not in peripheral blood mononuclear cells from healthy donors. Transient exposure to MLN4924 impaired colony formation in a dose-dependent manner. Kinetic analysis of drug-induced effects on cell cycle distribution revealed that AML cells treated with MLN4924 initially arrested at the G1 transition prior to their subsequent accumulation in the sub-G1 compartment. Assays conducted using MV-411 cells with and without stable shRNA-mediated knockdown of FLT3 expression demonstrated that MLN4924 is highly effective independent of FLT3 status. Further investigation revealed that the activity of MLN4924 was preserved when cells were co-cultured with bone marrow stromal cells indicating that it has the ability to overcome the effects of stromal-mediated survival signaling that has been established to blunt the efficacy of relevant standard of care agents. MLN4924 induced a dose and time dependant increase in the expression of phospo-IκB, an important target for degradation through the Nedd8 conjugation pathway. The inhibitory effects of MLN4924 on NFκB were confirmed by demonstrating that the transcriptional activity of the NFκB p65 subunit was significantly reduced following drug exposure. Moreover, treatment of immunodeficient mice implanted with HL-60 human leukemia cells with MLN4924 led to an inhibition of neddylated cullins, accumulation of phospho-IκBα and achieved complete and stable disease regression. Our results indicate that MLN4924 is a highly promising novel agent for the treatment of AML and warrants further evaluation in clinical trials. Disclosures: Smith: Millennium Pharmaceuticals: Employment. Gansey:Millennium Pharmaceuticals: Employment.
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Sandusky, Zachary. "Abstract 4033: A functional genome-wide screen to identify the ER degradation machinery in ER+ breast cancer cells." Cancer Research 82, no. 12_Supplement (June 15, 2022): 4033. http://dx.doi.org/10.1158/1538-7445.am2022-4033.
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Abstract Targeted protein degradation (TPD) is a new pharmaceutical strategy to hijack the ubiquitin-proteasome system to degrade target proteins. Many TPD drugs are discovered serendipitously, and we are only beginning to harness their potential. Understanding how TPD drugs co-opt the proteolysis pathway is important, as it could allow molecule re-engineering for TPD of new proteins (ie. neo-substrates). A rising example of TPD drugs are the selective estrogen receptor degraders (SERDs) - small molecule antagonists of estrogen receptor alpha (ER) that target ER protein for degradation. SERDs are the next generation of therapy for metastatic ER+ breast cancer. Currently, fulvestrant is the only FDA approved SERD, but fulvestrant is limited by poor pharmacokinetics and resistance conferred by ER mutations (ie. ER-Y537S). An intense pharmaceutical effort has developed five novel SERDs in phase three clinical trials. These novel SERDs have diverse side chains for inducing ER degradation but share advantages including non-steroidal structure, oral bioavailability, and activity against ER-Y537. Based on the diverse molecular properties of SERDs, I hypothesized they utilize different ubiquitin-proteasome pathway genes (such as E3 ligases) for ER degradation. To identify the machinery for SERD-mediated ER degradation, I designed a functional CRISPR/Cas9 screen, with highlights including a genome-wide gRNA library and measurement of endogenous ER protein in ER+ breast cancer cells. Initially focusing on genes required for fulvestrant-mediated ER degradation, we identified the proteolysis pathway as a top hit (q<5x10-6) including central genes in the ubiquitin-proteasome pathway (UBC, PSMA6, and NEDD8) and the ubiquitin-like SUMO pathway (UBC9 and RWDD3). Ubiquitin E3 ligases were also identified, including FBXO45 and VHL, which have been previously implicated as E3 ligases for ER. These hits were validated using inhibitors of ubiquitin-, NEDD8-, and SUMO-activating enzymes. These results demonstrate that multiple proteolysis mechanisms are sufficient for ER protein degradation. Currently, I am applying this screening approach to novel SERDs (such as elacestrant, amnecestrant, and giredestrant) to identify overlapping and unique mechanisms of degradation for wild-type ER and ER-Y537S. Importantly, understanding the mechanisms of these exciting new drugs will allow anticipation of resistance mechanisms in advanced ER+ breast cancer patients. Citation Format: Zachary Sandusky. A functional genome-wide screen to identify the ER degradation machinery in ER+ breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4033.
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Bramasole, Laylan, Abhishek Sinha, Dana Harshuk, Angela Cirigliano, Gurevich Sylvia, Zanlin Yu, Rinat Carmeli, Michael Glickman, Teresa Rinaldi, and Elah Pick. "The Proteasome Lid Triggers COP9 Signalosome Activity during the Transition of Saccharomyces cerevisiae Cells into Quiescence." Biomolecules 9, no. 9 (September 4, 2019): 449. http://dx.doi.org/10.3390/biom9090449.
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The class of Cullin–RING E3 ligases (CRLs) selectively ubiquitinate a large portion of proteins targeted for proteolysis by the 26S proteasome. Before degradation, ubiquitin molecules are removed from their conjugated proteins by deubiquitinating enzymes, a handful of which are associated with the proteasome. The CRL activity is triggered by modification of the Cullin subunit with the ubiquitin-like protein, NEDD8 (also known as Rub1 in Saccharomyces cerevisiae). Cullin modification is then reversed by hydrolytic action of the COP9 signalosome (CSN). As the NEDD8–Rub1 catalytic cycle is not essential for the viability of S. cerevisiae, this organism is a useful model system to study the alteration of Rub1–CRL conjugation patterns. In this study, we describe two distinct mutants of Rpn11, a proteasome-associated deubiquitinating enzyme, both of which exhibit a biochemical phenotype characterized by high accumulation of Rub1-modified Cdc53–Cullin1 (yCul1) upon entry into quiescence in S. cerevisiae. Further characterization revealed proteasome 19S-lid-associated deubiquitination activity that authorizes the hydrolysis of Rub1 from yCul1 by the CSN complex. Thus, our results suggest a negative feedback mechanism via proteasome capacity on upstream ubiquitinating enzymes.
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Szczepanowski, Roman H., Renata Filipek, and Matthias Bochtler. "Crystal Structure of a Fragment of Mouse Ubiquitin-activating Enzyme." Journal of Biological Chemistry 280, no. 23 (March 16, 2005): 22006–11. http://dx.doi.org/10.1074/jbc.m502583200.
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Protein ubiquitination requires the sequential activity of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin-ligase (E3). The ubiquitin-transfer machinery is hierarchically organized; for every ubiquitin-activating enzyme, there are several ubiquitin-conjugating enzymes, and most ubiquitin-conjugating enzymes can in turn interact with multiple ubiquitin ligases. Despite the central role of ubiquitin-activating enzyme in this cascade, a crystal structure of a ubiquitin-activating enzyme is not available. The enzyme is thought to consist of an adenylation domain, a catalytic cysteine domain, a four-helix bundle, and possibly, a ubiquitin-like domain. Its adenylation domain can be modeled because it is clearly homologous to the structurally known adenylation domains of the activating enzymes for the small ubiquitin-like modifier (SUMO) and for the protein encoded by the neuronal precursor cell-expressed, developmentally down-regulated gene 8 (NEDD8). Low sequence similarity and vastly different domain lengths make modeling difficult for the catalytic cysteine domain that results from the juxtaposition of two catalytic cysteine half-domains. Here, we present a biochemical and crystallographic characterization of the two half-domains and the crystal structure of the larger, second catalytic cysteine half-domain of mouse ubiquitin-activating enzyme. We show that the domain is organized around a conserved folding motif that is also present in the NEDD8- and SUMO-activating enzymes, and we propose a tentative model for full-length ubiquitin-activating enzyme.
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Huang, Tao, Zhengjun Gao, Yu Zhang, Keqi Fan, Fei Wang, Yiyuan Li, Jiangyan Zhong, et al. "CRL4DCAF2 negatively regulates IL-23 production in dendritic cells and limits the development of psoriasis." Journal of Experimental Medicine 215, no. 8 (July 17, 2018): 1999–2017. http://dx.doi.org/10.1084/jem.20180210.
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The E3 ligase CRL4DCAF2 is believed to be a pivotal regulator of the cell cycle and is required for mitotic and S phase progression. The NEDD8-targeting drug MLN4924, which inactivates cullin ring-finger ubiquitin ligases (CRLs), has been examined in clinical trials for various types of lymphoma and acute myeloid leukemia. However, the essential role of CRL4DCAF2 in primary myeloid cells remains poorly understood. MLN4924 treatment, which mimics DCAF2 depletion, also promotes the severity of mouse psoriasis models, consistent with the effects of reduced DCAF2 expression in various autoimmune diseases. Using transcriptomic and immunological approaches, we showed that CRL4DCAF2 in dendritic cells (DCs) regulates the proteolytic fate of NIK and negatively regulates IL-23 production. CRL4DCAF2 promoted the polyubiquitination and subsequent degradation of NIK independent of TRAF3 degradation. DCAF2 deficiency facilitated NIK accumulation and RelB nuclear translocation. DCAF2 DC-conditional knockout mice displayed increased sensitivity to autoimmune diseases. This study shows that CRL4DCAF2 is crucial for controlling NIK stability and highlights a unique mechanism that controls inflammatory diseases.
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Luke-Glaser, Sarah, Marcia Roy, Brett Larsen, Thierry Le Bihan, Pavel Metalnikov, Mike Tyers, Matthias Peter, and Lionel Pintard. "CIF-1, a Shared Subunit of the COP9/Signalosome and Eukaryotic Initiation Factor 3 Complexes, Regulates MEL-26 Levels in the Caenorhabditis elegans Embryo." Molecular and Cellular Biology 27, no. 12 (April 2, 2007): 4526–40. http://dx.doi.org/10.1128/mcb.01724-06.
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ABSTRACT The COP9/signalosome (CSN) is an evolutionarily conserved macromolecular complex that regulates the cullin-RING ligase (CRL) class of E3 ubiquitin ligases, primarily by removing the ubiquitin-like protein Nedd8 from the cullin subunit. In the Caenorhabditis elegans embryo, the CSN controls the degradation of the microtubule-severing protein MEI-1 through CUL-3 deneddylation. However, the molecular mechanisms of CSN function and its subunit composition remain to be elucidated. Here, using a proteomic approach, we have characterized the CSN and CUL-3 complexes from C. elegans embryos. We show that the CSN physically interacts with the CUL-3-based CRL and regulates its activity by counteracting the autocatalytic instability of the substrate-specific adaptor MEL-26. Importantly, we identified the uncharacterized protein K08F11.3/CIF-1 (for CSN-eukaryotic initiation factor 3 [eIF3]) as a stoichiometric and functionally important subunit of the CSN complex. CIF-1 appears to be the only ortholog of Csn7 encoded by the C. elegans genome, but it also exhibits extensive sequence similarity to eIF3m family members, which are required for the initiation of protein translation. Indeed, CIF-1 binds eIF-3.F and inactivation of cif-1 impairs translation in vivo. Taken together, our results indicate that CIF-1 is a shared subunit of the CSN and eIF3 complexes and may therefore link protein translation and degradation.
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Meister, Thieme, Thieme, Köhler, Schmitt, Valerius, and Braus. "COP9 Signalosome Interaction with UspA/Usp15 Deubiquitinase Controls VeA-Mediated Fungal Multicellular Development." Biomolecules 9, no. 6 (June 18, 2019): 238. http://dx.doi.org/10.3390/biom9060238.
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COP9 signalosome (CSN) and Den1/A deneddylases physically interact and promote multicellular development in fungi. CSN recognizes Skp1/cullin-1/Fbx E3 cullin-RING ligases (CRLs) without substrate and removes their posttranslational Nedd8 modification from the cullin scaffold. This results in CRL complex disassembly and allows Skp1 adaptor/Fbx receptor exchange for altered substrate specificity. We characterized the novel ubiquitin-specific protease UspA of the mold Aspergillus nidulans, which corresponds to CSN-associated human Usp15 and interacts with six CSN subunits. UspA reduces amounts of ubiquitinated proteins during fungal development, and the uspA gene expression is repressed by an intact CSN. UspA is localized in proximity to nuclei and recruits proteins related to nuclear transport and transcriptional processing, suggesting functions in nuclear entry control. UspA accelerates the formation of asexual conidiospores, sexual development, and supports the repression of secondary metabolite clusters as the derivative of benzaldehyde (dba) genes. UspA reduces protein levels of the fungal NF-kappa B-like velvet domain protein VeA, which coordinates differentiation and secondary metabolism. VeA stability depends on the Fbx23 receptor, which is required for light controlled development. Our data suggest that the interplay between CSN deneddylase, UspA deubiquitinase, and SCF-Fbx23 ensures accurate levels of VeA to support fungal development and an appropriate secondary metabolism.
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Nawrocki, Steffan T., Kevin R. Kelly, Kelli Oberheu, Devalingam Mahalingam, Peter G. Smith, and Jennifer S. Carew. "Disrupting NEDD8-Mediated Protein Turnover with MLN4924 Significantly Augments the Efficacy of Cytarabine." Blood 116, no. 21 (November 19, 2010): 3255. http://dx.doi.org/10.1182/blood.v116.21.3255.3255.
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Abstract Abstract 3255 Cytarabine-based therapy has been utilized in acute myeloid leukemia (AML) therapy for more than 30 years. However, the complete response (CR) rates are markedly inferior in older compared to younger patients with AML (45% versus 75%, respectively) due, in part, to the reduced ability of elderly patients to tolerate intensive therapy. Improving the outcomes for patients treated with cytarabine-based regimens represents a major clinical challenge in this disease. A randomized study of elderly patients with AML demonstrated that low dose cytarabine (LDAC) is superior to best supportive care. However, this regimen was not associated with any CRs in patients with adverse karyotype disease and/or poor baseline performance scores. Novel approaches are urgently needed to increase the efficacy of LDAC therapy for these patients. Timed protein destruction plays a crucial role in cellular homeostasis and is essential for many critical functions including cell cycle progression, signal transduction, and apoptosis. The processes that govern protein degradation frequently become dysregulated in cancer cells. Aberrant protein turnover contributes to disease progression, metastasis, and therapeutic resistance and therefore is an attractive target for selective pharmacological inhibition. The cullin-RING ubiquitin ligases (CRLs) are a subset of E3 ubiquitin ligases whose activity is regulated by modification with the ubiquitin-like molecule NEDD8. The CRLs control the ubiquitination and subsequent degradation of many proteins with important roles in cell cycle progression, DNA damage, stress responses, and signal transduction. MLN4924 is a potent and selective small molecule inhibitor of NEDD8 activating enzyme (NAE), the proximal regulator of the NEDD8 conjugation pathway, and has entered Phase I clinical trials for AML and other forms of cancer. Our earlier preclinical studies demonstrated that MLN4924 induced cell death in AML cell lines and primary patient specimens independent of FLT3 expression and stromal-mediated survival signaling and led to the stabilization of key NAE targets, inhibition of NF-kB activity, DNA damage, and reactive oxygen species generation. Notably, administration of MLN4924 to mice bearing AML xenografts was very well tolerated, led to stable disease regression and inhibition of NEDDylated cullins. Based on the high tolerability, potency, and multifaceted mechanism of action of MLN4924, we hypothesized that it may significantly augment the efficacy of the standard agent cytarabine. To test our hypothesis, we first investigated the effects of this therapeutic combination on cell viability, clonogenic survival, and apoptosis induction in a panel of AML cell lines. MLN4924 cooperated with cytarabine to significantly reduce cell viability, inhibit clonogenic survival, and induce mitochondrial-dependent apoptosis. The addition of MLN4924 did not significantly alter the sensitivity of normal peripheral blood mononuclear cells from healthy donors to cytarabine, indicating that this combination may have therapeutic selectivity. Immunoblotting analyses revealed that MLN4924 enhanced cytarabine-induced stabilization of the NEDD8 target and cell cycle regulator, p27. The MLN4924/cytarabine combination also promoted increased phosphorylation of the DNA damage response regulator Chk1. Targeted knockdown of Chk1 demonstrated a critical role for Chk1 as a mediator of the pro-apoptotic effects of this combination. In vivo examining the combination is in progress and will be presented. Our collective findings suggest that combining the novel NAE inhibitor MLN4924 with cytarabine is a promising strategy for AML therapy that warrants further investigation. Disclosures: Smith: Millennium Pharmaceuticals, Inc.: Employment.
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Ochiiwa, Hiroaki, Guzhanuer Ailiken, Masataka Yokoyama, Kazuyuki Yamagata, Hidekazu Nagano, Chihoko Yoshimura, Hiromi Muraoka, et al. "TAS4464, a NEDD8-activating enzyme inhibitor, activates both intrinsic and extrinsic apoptotic pathways via c-Myc-mediated regulation in acute myeloid leukemia." Oncogene 40, no. 7 (January 8, 2021): 1217–30. http://dx.doi.org/10.1038/s41388-020-01586-4.
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AbstractTAS4464, a potent, selective small molecule NEDD8-activating enzyme (NAE) inhibitor, leads to inactivation of cullin-RING E3 ubiquitin ligases (CRLs) and consequent accumulations of its substrate proteins. Here, we investigated the antitumor properties and action mechanism of TAS4464 in acute myeloid leukemia (AML). TAS4464 induced apoptotic cell death in various AML cell lines. TAS4464 treatments resulted in the activation of both the caspase-9-mediated intrinsic apoptotic pathway and caspase-8-mediated extrinsic apoptotic pathway in AML cells; combined treatment with inhibitors of these caspases markedly diminished TAS4464-induced apoptosis. In each apoptotic pathway, TAS4464 induced the mRNA transcription of the intrinsic proapoptotic factor NOXA and decreased that of the extrinsic antiapoptotic factor c-FLIP. RNA-sequencing analysis showed that the signaling pathway of the CRL substrate c-Myc was enriched after TAS4464 treatment. Chromatin immunoprecipitation (ChIP) assay revealed that TAS4464-induced c-Myc bound to the PMAIP1 (encoding NOXA) and CFLAR (encoding c-FLIP) promoter regions, and siRNA-mediated c-Myc knockdown neutralized both TAS4464-mediated NOXA induction and c-FLIP downregulation. TAS4464 activated both caspase-8 and caspase-9 along with an increase in NOXA and a decrease in c-FLIP, resulting in complete tumor remission in a human AML xenograft model. These findings suggest that NAE inhibition leads to anti-AML activity via a novel c-Myc-dependent apoptosis induction mechanism.
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Sheedlo, Michael J., Jiazhang Qiu, Yunhao Tan, Lake N. Paul, Zhao-Qing Luo, and Chittaranjan Das. "Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination." Proceedings of the National Academy of Sciences 112, no. 49 (November 23, 2015): 15090–95. http://dx.doi.org/10.1073/pnas.1514568112.
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Manipulation of the host’s ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well known, as are a variety of viral deubiquitinases (DUBs). Bacterial DUBs have been discovered, but little is known about the structure and mechanism underlying their ubiquitin recognition. In this report, we found that members of theLegionella pneumophilaSidE effector family harbor a DUB module important for ubiquitin dynamics on the bacterial phagosome. Structural analysis of this domain alone and in complex with ubiquitin vinyl methyl ester (Ub-VME) reveals unique molecular contacts used in ubiquitin recognition. Instead of relying on the Ile44 patch of ubiquitin, as commonly used in eukaryotic counterparts, the SdeADubmodule engages Gln40 of ubiquitin. The architecture of the active-site cleft presents an open arrangement with conformational plasticity, permitting deubiquitination of three of the most abundant polyubiquitin chains, with a distinct preference for Lys63 linkages. We have shown that this preference enables efficient removal of Lys63 linkages from the phagosomal surface. Remarkably, the structure reveals by far the most parsimonious use of molecular contacts to achieve deubiquitination, with less than 1,000 Å2of accessible surface area buried upon complex formation with ubiquitin. This type of molecular recognition appears to enable dual specificity toward ubiquitin and the ubiquitin-like modifier NEDD8.
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Yao, Lintong, and HaiYu Zhou. "A potential mechanism of ferroptosis modulation for immunotherapy in LUAD: ceRNAs networks of OTUD6B-AS1 modulate the balance of ubiquitination." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e15111-e15111. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e15111.
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e15111 Background: Ferroptosis plays a pivotal role in cancer progression and therapeutic response of immunotherapy in lung adenocarcinoma (LUAD). Recent studies on ferroptosis regulation by lncRNAs were conducted sporadically. Our study explored FrlncRNAs in LUAD comprehensively, exploring functional mechanisms and verified the correlation between ferroptosis and ubiquitination. Methods: Data of LUAD samples were download from GEO and TCGA databases. Annotated ferroptosis-related genes were retrieved from FerrDb and GeneCards databases. Ferroptosis-related lncRNA (FrlncRNAs) was identified by correlation analysis. The LASSO analysis and cox regression analysis were performed to filtrate significant prognostic FrlncRNAs, followed with model construction and patient stratification. Tumor immune microenvironment, functional pathways were investigated. Subcellular location and potential competing endogenous RNAs (ceRNAs) mechanisms were predicted by GDCRNATools algorithm. Results: Ferroptosis-related prognostic model constructed by 14 FrlncRNAs signature showed high prognostic efficacy with significant survival difference and robust area under the curve (AUC for 5 years survival: 0.89 in training cohort and 0.87 in validation cohort). Higher proportion of myeloid-derived suppressor cells were detected in high-risk group, of which ferroptotic status were supressed. Ferroptosis-enhanced samples harboured higher expression of immune checkpoints such as PD-L1, CTLA-4, TIM3 and CD47 and immune-recruiting interleukins such as IL2, IL4, IL7. Reasonably, more potential responders to immunotherapy were predicted in ferroptosis-enhanced samples. Considering the subcellular location, potential mechanism of ceRNA network was predicted that OTUD6B-AS1 may compete with mir-144 to regulate or modify NUDCD1 and MARCH7 through miRNA sponge. OTUD6B-AS1 encodes the protein of ovarian tumor domain deubiquitinase 6B, while MARCH7 contributes to a RING domain of membrane bound E3 ubiquitin ligases. GO, KEGG and GSEA pathway analyses focused on ubiquitin-protein transferase activity, polyubiquitination, mTOR, Hippo and NOTCH pathways. Protein-protein interaction identified hub genes in ferroptotic regulation such as NEDD8 and HERC2, which were coding genes of ubiquitin ligase E3 as well. Hence, the balance of ubiquitination and deubiquitination induced by the interplay of ceRNA network could be pivotal process in ferroptosis modulation in LUAD. Conclusions: In summary, we reveal potential mechanisms that OTUD6B-AS1 may compete with mir-144 to regulate the expression NUDCD1 and MARCH7 through miRNA sponge or modifying protein structures, modulating ferroptosis by balance of ubiquitination and deubiquitination. Ferroptosis may participate in the recruitment of immune system and portrait of tumor immune microenvironment.
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Kittai, Adam, Scott R. Best, Taylor Rowland, Nur Bruss, Craig Okada, and Alexey V. Danilov. "Pevonedistat, a Small Molecule Inhibitor of NEDD8-Activating Enzyme (NAE), Induces Cell Cycle Deregulation, Anaphase Catastrophe, and Apoptosis in T-Cell Lymphoma Cells." Blood 132, Supplement 1 (November 29, 2018): 1667. http://dx.doi.org/10.1182/blood-2018-99-113179.
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Abstract Introduction: Despite the significant progress of targeted therapies in B-cell malignancies, T-cell lymphomas remain an area of unmet medical need. Most patients are diagnosed at an advanced stage and have limited treatment options. Moreover, most patients who relapse following initial chemotherapy ultimately succumb to disease. Recent successes of targeting the proteasome (i.e., bortezomib) and E3 ligases (i.e., lenalidomide) identify the ubiquitin-proteasome system (UPS) as a tractable target in lymphoma. Pevonedistat, an investigational small molecule inhibitor of NEDD8-activating enzyme (NAE), interferes with activation of NEDD8, a ubiquitin-like modifier. This interference ultimately leads to decreased activity of cullin-RING (E3) ligases and accumulation of their substrates, including inhibitor of NFκB (IκB), the replication licensing protein Cdt1, and p27. We previously demonstrated that targeting NAE affected primary neoplastic B cells via several mechanisms: disruption of NFκB activity as well as induction of Cdt1, DNA damage, and cell cycle arrest. Here, we demonstrate that targeting NAE in T-cell lymphoma cells mediates apoptosis via cell cycle deregulation, accompanied by induction of Cdt1 and p27, and induction of anaphase catastrophe. Methods: Experiments were performed in T-cell lymphoma cell lines (SR, HH, Jurkat, and SUP-T1) as well as circulating primary cells from patients with peripheral T-cell lymphoma and Sezary syndrome. Pevonedistat (TAK-924) was obtained from Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited (Cambridge, MA). Apoptosis was assessed by Annexin V staining. Results: SR (PTCL) cells and primary T-cell lymphoma cells were the most sensitive to pevonedistat (IC50of ~250nM at 24 hours); Jurkat and SUP-T1 cells demonstrated low/intermediate sensitivity, whereas HH (CTCL) cells were resistant. Targeting NAE disrupted cullin neddylation in a dose-dependent manner across all tested cell lines and primary neoplastic T cells, followed by accumulation of phospho-IκBα. Upregulation of phospho-IκBα was notable within 2 hours of pevonedistat treatment across both sensitive and resistant cell lines and primary cells. Concomitantly, we observed induction of p27 and Cdt1. Upregulation of Cdt1 was attenuated in HH cells compared with SR, consistent with the low proliferation rate of the former. Treatment of SR cells with pevonedistat led to DNA damage as evidenced by γH2AX and G2/M arrest. Chromosomal instability is a prominent feature in cancer and poorly studied as a therapeutic target. We have previously shown that cancer cells undergo multipolar anaphase in response to inhibition of cyclin-dependent kinase-2 (CDK2), an interphase CDK, followed by apoptosis and termed this event anaphase catastrophe (Hu et al., 2015; Danilov et al., 2016). As we observed robust accumulation of the endogenous CDK inhibitor p27 in cells treated with pevonedistat, an event presumed to lead to attenuated CDK2 activity, we studied anaphase catastrophe in this setting. We visualized anaphase catastrophe by immunofluorescent staining for nuclear material (DAPI) and γ-tubulin, and scored it in 50 cells per condition. NAE inhibition with pevonedistat induced anaphase catastrophe in SR and Jurkat cells. Upon 24-hour exposure to 250 nM pevonedistat, 9.8±6.0% of SR and 18±4.4% of Jurkat cells demonstrated multipolar anaphases, compared with 1±0.8% and 3.0±2.6% with vehicle control, respectively. Conclusions: Inhibiting NAE with pevonedistat induces apoptosis of T-cell lymphoma cells. We propose deregulation of Cdt1 and p27, followed by anaphase catastrophe, as a key mechanistic event implicated in pevonedistat-induced apoptosis in neoplastic T cells. Our work provides rationale to further investigate neddylation as a therapeutic target in T-cell lymphoma. Disclosures Danilov: Verastem: Consultancy, Research Funding; TG Therapeutics: Consultancy; Genentech: Consultancy, Research Funding; Takeda Oncology: Research Funding; Gilead Sciences: Consultancy, Research Funding; Astra Zeneca: Consultancy; Aptose Biosciences: Research Funding; Bayer Oncology: Consultancy, Research Funding.
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Medvar, Barbara, Viswanathan Raghuram, Trairak Pisitkun, Abhijit Sarkar, and Mark A. Knepper. "Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation." Physiological Genomics 48, no. 7 (July 1, 2016): 502–12. http://dx.doi.org/10.1152/physiolgenomics.00031.2016.
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Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, “What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?” using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database ( https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/ ). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover.
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Jiang, Hanjie, Stefani N. Thomas, Zan Chen, Claire Y. Chiang, and Philip A. Cole. "Comparative analysis of the catalytic regulation of NEDD4-1 and WWP2 ubiquitin ligases." Journal of Biological Chemistry 294, no. 46 (October 2, 2019): 17421–36. http://dx.doi.org/10.1074/jbc.ra119.009211.
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NEDD4-1 E3 ubiquitin protein ligase (NEDD4-1) and WW domain-containing E3 ubiquitin ligase (WWP2) are HECT family ubiquitin E3 ligases. They catalyze Lys ubiquitination of themselves and other proteins and are important in cell growth and differentiation. Regulation of NEDD4-1 and WWP2 catalytic activities is important for controlling cellular protein homeostasis, and their dysregulation may lead to cancer and other diseases. Previous work has implicated noncatalytic regions, including the C2 domain and/or WW domain linkers in NEDD4-1 and WWP2, in contributing to autoinhibition of the catalytic HECT domains by intramolecular interactions. Here, we explored the molecular mechanisms of these NEDD4-1 and WWP2 regulatory regions and their interplay with allosteric binding proteins such as Nedd4 family-interacting protein (NDFIP1), engineered ubiquitin variants, and linker phosphomimics. We found that in addition to influencing catalytic activities, the WW domain linker regions in NEDD4-1 and WWP2 can impact product distribution, including the degree of polyubiquitination and Lys-48 versus Lys-63 linkages. We show that allosteric activation by NDFIP1 or engineered ubiquitin variants is largely mediated by relief of WW domain linker autoinhibition. WWP2-mediated ubiquitination of WW domain-binding protein 2 (WBP2), phosphatase and tensin homolog (PTEN), and p62 proteins by WWP2 suggests that substrate ubiquitination can also be influenced by WW linker autoinhibition, although to differing extents. Overall, our results provide a deeper understanding of the intricate and multifaceted set of regulatory mechanisms in the control of NEDD4-1–related ubiquitin ligases.
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Qian, Hao, Ying Zhang, Boquan Wu, Shaojun Wu, Shilong You, Naijin Zhang, and Yingxian Sun. "Structure and function of HECT E3 ubiquitin ligases and their role in oxidative stress." Journal of Translational Internal Medicine 8, no. 2 (June 30, 2020): 71–79. http://dx.doi.org/10.2478/jtim-2020-0012.
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AbstractUbiquitination is a modification after protein transcription that plays a vital role in maintaining the homeostasis of the cellular environment. The Homologous to E6AP C-terminus (HECT) family E3 ubiquitin ligases are a kind of E3 ubiquitin ligases with a C-terminal HECT domain that mediates the binding of ubiquitin to substrate proteins and a variable-length N-terminal extension. HECT-ubiquitinated ligases can be divided into three categories: NEDD4 superfamily, HERC superfamily, and other HECT superfamilies. HECT ubiquitin ligase plays an essential role in the development of many human diseases. In this review, we focus on the physiological and pathological processes involved in oxidative stress and the role of E3 ubiquitin ligase of the HECT family.
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Sicari, Daria, Janine Weber, Elena Maspero, and Simona Polo. "The NEDD4 ubiquitin E3 ligase: a snapshot view of its functional activity and regulation." Biochemical Society Transactions 50, no. 1 (February 7, 2022): 473–85. http://dx.doi.org/10.1042/bst20210731.
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Due to its fundamental role in all eukaryotic cells, a deeper understanding of the molecular mechanisms underlying ubiquitination is of central importance. Being responsible for chain specificity and substrate recognition, E3 ligases are the selective elements of the ubiquitination process. In this review, we discuss different cellular pathways regulated by one of the first identified E3 ligase, NEDD4, focusing on its pathophysiological role, its known targets and modulators. In addition, we highlight small molecule inhibitors that act on NEDD4 and discuss new strategies to effectively target this E3 enzyme.
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Conway, James A., Grant Kinsman, and Edgar R. Kramer. "The Role of NEDD4 E3 Ubiquitin–Protein Ligases in Parkinson’s Disease." Genes 13, no. 3 (March 14, 2022): 513. http://dx.doi.org/10.3390/genes13030513.
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Parkinson’s disease (PD) is a debilitating neurodegenerative disease that causes a great clinical burden. However, its exact molecular pathologies are not fully understood. Whilst there are a number of avenues for research into slowing, halting, or reversing PD, one central idea is to enhance the clearance of the proposed aetiological protein, oligomeric α-synuclein. Oligomeric α-synuclein is the main constituent protein in Lewy bodies and neurites and is considered neurotoxic. Multiple E3 ubiquitin-protein ligases, including the NEDD4 (neural precursor cell expressed developmentally downregulated protein 4) family, parkin, SIAH (mammalian homologues of Drosophila seven in absentia), CHIP (carboxy-terminus of Hsc70 interacting protein), and SCFFXBL5 SCF ubiquitin ligase assembled by the S-phase kinase-associated protein (SKP1), cullin-1 (Cul1), a zinc-binding RING finger protein, and the F-box domain/Leucine-rich repeat protein 5-containing protein FBXL5), have been shown to be able to ubiquitinate α-synuclein, influencing its subsequent degradation via the proteasome or lysosome. Here, we explore the link between NEDD4 ligases and PD, which is not only via α-synuclein but further strengthened by several additional substrates and interaction partners. Some members of the NEDD4 family of ligases are thought to crosstalk even with PD-related genes and proteins found to be mutated in familial forms of PD. Mutations in NEDD4 family genes have not been observed in PD patients, most likely because of their essential survival function during development. Following further in vivo studies, it has been thought that NEDD4 ligases may be viable therapeutic targets in PD. NEDD4 family members could clear toxic proteins, enhancing cell survival and slowing disease progression, or might diminish beneficial proteins, reducing cell survival and accelerating disease progression. Here, we review studies to date on the expression and function of NEDD4 ubiquitin ligases in the brain and their possible impact on PD pathology.
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Yang, Cheng-Wei, Yue-Zhi Lee, Hsing-Yu Hsu, Guan-Hao Zhao, and Shiow-Ju Lee. "Tyrphostin AG1024 Suppresses Coronaviral Replication by Downregulating JAK1 via an IR/IGF-1R Independent Proteolysis Mediated by Ndfip1/2_NEDD4-like E3 Ligase Itch." Pharmaceuticals 15, no. 2 (February 17, 2022): 241. http://dx.doi.org/10.3390/ph15020241.
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JAK1 depletion or downregulation was previously reported to account for coronavirus inhibition. Here, we found that AG1024, an IR (insulin receptor) and IGF-1R (insulin-like growth factor 1 receptor) inhibitor, diminishes JAK1 protein levels and exerts anti-coronaviral activities with EC50 values of 5.2 ± 0.3 μM against transmissible gastroenteritis coronavirus (TGEV) and 4.3 ± 0.3 μM against human flu coronavirus OC43. However, although the IR and IGF-1R signaling pathways are activated by insulin or IGF-1 in swine testis cells, they are not triggered upon TGEV infection. AG1024, therefore, inhibits coronaviral replication and downregulates JAK1 protein levels independently of IR and IGF-1R. Moreover, JAK1 proteolysis caused by AG1024 was found through activation of upstream Ndfip1/2 and its effector NEDD4-like E3 ligase Itch. In addition, ouabain, which was reported to mediate JAK1 proteolysis causing anti-coronaviral activity by activation of Ndfip1/2 and NEDD4 E3 ligase, additively inhibited anti-coronaviral activity and JAK1 diminishment in combination with AG1024. This study provides novel insights into the pharmacological effects of AG1024 and Itch E3 ligase mediated JAK1 proteolysis and identified Ndfip1/2 as a cognate effector for JAK1 proteolysis via the diversified E3 ligases NEDD4 and NEDD4-like Itch. These findings are expected to provide valued information for the future development of anti-viral agents.
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Bruce, M. Christine, Voula Kanelis, Fatemeh Fouladkou, Anne Debonneville, Olivier Staub, and Daniela Rotin. "Regulation of Nedd4-2 self-ubiquitination and stability by a PY motif located within its HECT-domain." Biochemical Journal 415, no. 1 (September 12, 2008): 155–63. http://dx.doi.org/10.1042/bj20071708.
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Ubiquitin ligases play a pivotal role in substrate recognition and ubiquitin transfer, yet little is known about the regulation of their catalytic activity. Nedd4 (neural-precursor-cell-expressed, developmentally down-regulated 4)-2 is an E3 ubiquitin ligase composed of a C2 domain, four WW domains (protein–protein interaction domains containing two conserved tryptophan residues) that bind PY motifs (L/PPXY) and a ubiquitin ligase HECT (homologous with E6-associated protein C-terminus) domain. In the present paper we show that the WW domains of Nedd4-2 bind (weakly) to a PY motif (LPXY) located within its own HECT domain and inhibit auto-ubiquitination. Pulse–chase experiments demonstrated that mutation of the HECT PY-motif decreases the stability of Nedd4-2, suggesting that it is involved in stabilization of this E3 ligase. Interestingly, the HECT PY-motif mutation does not affect ubiquitination or down-regulation of a known Nedd4-2 substrate, ENaC (epithelial sodium channel). ENaC ubiquitination, in turn, appears to promote Nedd4-2 self-ubiquitination. These results support a model in which the inter- or intra-molecular WW-domain–HECT PY-motif interaction stabilizes Nedd4-2 by preventing self-ubiquitination. Substrate binding disrupts this interaction, allowing self-ubiquitination of Nedd4-2 and subsequent degradation, resulting in down-regulation of Nedd4-2 once it has ubiquitinated its target. These findings also point to a novel mechanism employed by a ubiquitin ligase to regulate itself differentially compared with substrate ubiquitination and stability.
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Alrosan, Amjad, Shereen M. Aleidi, Alryel Yang, Andrew J. Brown, and Ingrid C. Gelissen. "The Adaptor Protein Alix is Involved in the Interaction Between the Ubiquitin Ligase NEDD4-1 and its Targets, ABCG1 and ABCG4." International Journal of Molecular Sciences 20, no. 11 (June 2, 2019): 2714. http://dx.doi.org/10.3390/ijms20112714.
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Several ATP-Binding Cassette (ABC) transporters, including ABCG1 and the related ABCG4, are essential regulators of cellular lipid homeostasis. ABCG1 is expressed ubiquitously and is functional in the context of atherosclerosis. However, ABCG4 is expressed almost exclusively in brain and has been linked to Alzheimer’s disease (AD). These transporters are highly regulated post-translationally by E3 ubiquitin ligases, with the ligase NEDD4-1 (Neural precursor cell-expressed developmentally downregulated gene 4) implicated in their protein stability. In this study, we investigated interacting partners of ABCG1 using peptide-mass spectrometry and identified the potential adaptor protein, Alix (apoptosis-linked gene 2-interacting protein X). In this paper, we hypothesized and investigated whether Alix could facilitate the interaction between NEDD4-1 and the ABC transporters. We showed that Alix and NEDD4-1 proteins were co-expressed in several commonly used cell lines. Knockdown of Alix in cells overexpressing ABCG1 or ABCG4 increased transporter protein expression while co-immunoprecipitation experiments showed interaction between NEDD4-1, Alix, and ABC transporters. In summary, we provide evidence that Alix serves as a co-factor for the interaction between the E3-ubiquitin ligase NEDD4-1 and the ABC transporter targets, ABCG1 and ABCG4.
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Han, Ziying, Cari A. Sagum, Mark T. Bedford, Sachdev S. Sidhu, Marius Sudol, and Ronald N. Harty. "ITCH E3 Ubiquitin Ligase Interacts with Ebola Virus VP40 To Regulate Budding." Journal of Virology 90, no. 20 (August 3, 2016): 9163–71. http://dx.doi.org/10.1128/jvi.01078-16.
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ABSTRACTEbola virus (EBOV) and Marburg virus (MARV) belong to theFiloviridaefamily and can cause outbreaks of severe hemorrhagic fever, with high mortality rates in humans. The EBOV VP40 (eVP40) and MARV VP40 (mVP40) matrix proteins play a central role in virion assembly and egress, such that independent expression of VP40 leads to the production and egress of virus-like particles (VLPs) that accurately mimic the budding of infectious virus. Late (L) budding domains of eVP40 recruit host proteins (e.g., Tsg101, Nedd4, and Alix) that are important for efficient virus egress and spread. For example, the PPxY-type L domain of eVP40 and mVP40 recruits the host Nedd4 E3 ubiquitin ligase via its WW domains to facilitate budding. Here we sought to identify additional WW domain host interactors and demonstrate that the PPxY L domain motif of eVP40 interacts specifically with the WW domain of the host E3 ubiquitin ligase ITCH. ITCH, like Nedd4, is a member of the HECT class of E3 ubiquitin ligases, and the resultant physical and functional interaction with eVP40 facilitates VLP and virus budding. Identification of this novel eVP40 interactor highlights the functional interplay between cellular E3 ligases, ubiquitination, and regulation of VP40-mediated egress.IMPORTANCEThe unprecedented magnitude and scope of the recent 2014-2015 EBOV outbreak in West Africa and its emergence here in the United States and other countries underscore the critical need for a better understanding of the biology and pathogenesis of this emerging pathogen. We have identified a novel and functional EBOV VP40 interactor, ITCH, that regulates VP40-mediated egress. This virus-host interaction may represent a new target for our previously identified small-molecule inhibitors of virus egress.
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Wang, Chenji, Jian An, Pingzhao Zhang, Chen Xu, Kun Gao, Di Wu, Dejie Wang, Hongxiu Yu, Jun O. Liu, and Long Yu. "The Nedd4-like ubiquitin E3 ligases target angiomotin/p130 to ubiquitin-dependent degradation." Biochemical Journal 444, no. 2 (May 11, 2012): 279–89. http://dx.doi.org/10.1042/bj20111983.
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AMOT (angiomotin) is a membrane-associated protein that is expressed in ECs (endothelial cells) and controls migration, TJ (tight junction) formation, cell polarity and angiogenesis. Recent studies have revealed that AMOT and two AMOT-like proteins, AMOTL1 and AMOTL2, play critical roles in the Hippo pathway by regulating the subcellular localization of the co-activators YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif). However, it has been unclear how AMOT is regulated. In the present study, we report that AMOT undergoes proteasomal degradation. We identify three members of Nedd4 (neural-precursor-cell-expressed developmentally down-regulated)-like ubiquitin E3 ligases, Nedd4, Nedd4-2 and Itch, as the ubiquitin E3 ligases for the long isoform of AMOT, AMOT/p130. We demonstrate that Nedd4, Nedd4-2 and Itch mediate poly-ubiquitination of AMOT/p130 in vivo. Overexpression of Nedd4, Nedd4-2 or Itch leads to AMOT/p130 proteasomal degradation. Knockdown of Nedd4, Nedd4-2 and Itch causes an accumulation of steady-state level of AMOT/p130. We also show that three L/P-PXY motifs of AMOT/p130 and the WW domains of Nedd4 mediate their interaction. Furthermore, Nedd4-like ubiquitin E3 ligases might compete with YAP for the binding to AMOT/p130, and subsequently targeting AMOT/p130 for ubiquitin-dependent degradation. Together, these observations reveal a novel post-translational regulatory mechanism of AMOT/p130.
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Xu, Ke, Yanhao Chu, Qin Liu, Wenguo Fan, Hongwen He, and Fang Huang. "NEDD4 E3 Ligases: Functions and Mechanisms in Bone and Tooth." International Journal of Molecular Sciences 23, no. 17 (September 1, 2022): 9937. http://dx.doi.org/10.3390/ijms23179937.
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Protein ubiquitination is a precisely controlled enzymatic cascade reaction belonging to the post-translational modification of proteins. In this process, E3 ligases catalyze the binding of ubiquitin (Ub) to protein substrates and define specificity. The neuronally expressed developmentally down-regulated 4 (NEDD4) subfamily, belonging to the homology to E6APC terminus (HECT) class of E3 ligases, has recently emerged as an essential determinant of multiple cellular processes in different tissues, including bone and tooth. Here, we place special emphasis on the regulatory role of the NEDD4 subfamily in the molecular and cell biology of osteogenesis. We elucidate in detail the specific roles, downstream substrates, and upstream regulatory mechanisms of the NEDD4 subfamily. Further, we provide an overview of the involvement of E3 ligases and deubiquitinases in the development, repair, and regeneration of another mineralized tissue—tooth.
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Wang, Xiaoguang, Vi Lam, Dan Vuong, Tingting Liu, Olga Danilova, Tanya Siddiqi, Allison J. Berger, Lili Wang, and Alexey V. Danilov. "Nedd8-Activating Enzyme Inhibition Enhances Anti-Tumor Immunity and PD1 Blockade in In Vivo lymphoma Models." Blood 138, Supplement 1 (November 5, 2021): 2414. http://dx.doi.org/10.1182/blood-2021-146349.
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Abstract Introduction: Immune checkpoint inhibitors have limited single agent activity in B-cell non-Hodgkin lymphoma (NHL). Hence, it is important to develop strategies which will thwart immune evasion in this disease. Neddylation is a sequential enzyme-based process which ultimately regulates protein turnover. In the initial step, NAE activates NEDD8 in an ATP-dependent reaction in which a high-energy thioester bond is formed between NEDD8 and the catalytic cysteine of NAE. Active NEDD8 is then transferred to the NEDD8-specific E2 conjugating enzyme (UBE2M) and is conjugated to cullin proteins which are part of the Cullin-RING E3 ubiquitin ligases (CRL). Pevonedistat (pevo) forms a covalent adduct with NEDD8, thereby inhibiting NAE and thus reduces CRL activity and diminishes ubiquitination and proteasomal degradation of CRL substrates (IκB, HIF-1α, etc). We have recently reported that neddylation regulates T cell activation and polarization (Best et al, Leukemia 2021). Here we investigate how pharmacologic targeting of neddylation modulates anti-tumor immunity using NHL models. Methods: Peripheral blood mononuclear cells were isolated from patients with NHL and T cells were purified using Dynabeads. A20 cells were transplanted into flanks of syngeneic BALB/c mice. When tumors reached 100 mm 3, mice were randomized into groups and treated with pevo 60 mg/kg subcutaneously daily for 10 days or vehicle control. Once moribund, mice were sacrificed, tumors were processed into single-cell suspension and analyzed by flow cytometry. Pevo was provided by Takeda Development Center Americas Inc. (Cambridge, MA). Results: Primary patient-derived CD3/28-stimulated CD3 + T cells exhibited upregulation of TNFα and IFNγ in vitro in the presence of pevo. Concurrently, we observed increased expression of PD-1 and CTLA-4. Pre-treatment of T cells with pevo enhanced killing of NHL cell lines (JeKo-1, Mino, Maver-1 and VAL) in allogeneic cytotoxicity assays. Expectedly, treatment with pevo resulted in increased expression of HIF-1α in TCR-stimulated T cells. shRNA-mediated knockdown of HIF-1α abrogated the pevo effect, suggesting that NAE inhibition modulates T cell function in HIF-1α-dependent manner. While A20 cells showed resistance in vitro, treatment with pevo delayed lymphoma progression in A20 mice in vivo (Fig 1A). This was accompanied by an increase of tumor-infiltrating lymphocytes (TILs; Fig 1B). CD8 + TILs from pevo-treated mice exhibited activated phenotype as manifested by increased secretion of IFNγ (Fig 1C). Meanwhile, expression of the exhaustion molecules CTLA-4 and PD-1 by CD4/CD8 + TILs remained unchanged. To further investigate the role of T-cell immunity in this setting, we employed 1) CD8 depletion by pre-treatment with 12.5 mg/kg anti-CD8 antibody (IV); or 2) CRISPR/Cas9-mediated knockout of β2-microglobulin (MHC class I protein) in A20 cells. Either approach led to a partial decrease of pevo efficacy in vivo compared with respective controls. To exclude tumor-intrinsic effect of NAE inhibition, we knocked down UBE2M in A20 cells. Loss of UBE2M had no effect on growth of control tumors, or pevo therapeutic effect, implying that the anti-tumor efficacy of NAEi was T cell-mediated in this model. Since pevo modulates PD-1 on human T cells, we explored its effect on PD-L1 expression. Treatment with pevo upregulated PD-L1 expression in A20 cells in a MYC-dependent manner. Hence, we explored a combination of pevo and αPD-1 blockade in A20 model. Combination treatment significantly increased the CD4 + and CD8 + TILs. A decrease in tumor growth was significantly more pronounced than with either drug alone (Fig 1A). The combination benefit was fully reversed by loss of B2M, again highlighting the importance of immune mechanism . We observed expansion of IL-2, IL-4 and IL-17-secreting CD4+ TILs following the combined treatment, compared with either drug alone. In addition, CD4+ and CD8+ TILs derived from these mice secreted high levels of IFNγ (Fig. 1C). Conclusions: NAE inhibition enhanced T cell-mediated cytotoxicity in vitro. Treatment with pevo promoted activation of TILs and restricted tumor growth in an A20 mouse lymphoma model. Pevo-treated tumors were sensitized to αPD-1 . Thus, targeting NAE enhances anti-tumor immunity. Our data provide a strong rationale for future studies of pevo in combination with immune checkpoint inhibitors in lymphoma and other tumors. Figure 1 Figure 1. Disclosures Siddiqi: Juno Therapeutics: Membership on an entity's Board of Directors or advisory committees, Research Funding; BeiGene: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; TG Therapeutics: Research Funding; Pharmacyclics LLC, an AbbVie Company: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen: Speakers Bureau; AstraZeneca: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Celgene: Membership on an entity's Board of Directors or advisory committees; Kite Pharma: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncternal: Research Funding. Berger: Takeda Development Center Americas, Inc.: Current Employment. Danilov: Bayer Oncology: Consultancy, Honoraria, Research Funding; SecuraBio: Research Funding; Genentech: Consultancy, Honoraria, Research Funding; TG Therapeutics: Consultancy, Research Funding; Abbvie: Consultancy, Honoraria; Beigene: Consultancy, Honoraria; Pharmacyclics: Consultancy, Honoraria; Gilead Sciences: Research Funding; Takeda Oncology: Research Funding; Astra Zeneca: Consultancy, Honoraria, Research Funding; Bristol-Meyers-Squibb: Honoraria, Research Funding; Rigel Pharm: Honoraria.
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O'Leary, Claire, Chris Riling, and Paula Oliver. "Nedd4-family interacting proteins activate Nedd4-family E3 ubiquitin ligases in T cells to limit pathogenic inflammation. (P1382)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 203.8. http://dx.doi.org/10.4049/jimmunol.190.supp.203.8.
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Abstract E3 ubiquitin ligases tune signaling pathways in activated T cells to regulate differentiation and cytokine production. Nedd4-family ligases have distinct roles in these processes. These ligases often function with adaptors, which have been shown to aid binding to substrates and/or E2 enzymes. We have found that Nedd4-family interacting protein 1 (Ndfip1) and Ndfip2 promote Nedd4-family E3 ligase catalytic activity by a new mechanism. Our in vitro studies also indicate that Ndfip1 and Ndfip2 have overlapping function. In vivo, Ndfip1 negatively regulates T cell activation and TH2 cytokine production. The in vivo function of Ndfip2 is unknown; therefore, we generated Ndfip2-/- mice. Our studies revealed that, unlike Ndfip1, Ndfip2 is not a prominent negative regulator of T cell activation or TH2 polarization. However, loss of Ndfip2 exacerbated the inflammatory Ndfip1-/- phenotype. This suggested that, like Ndfip1, Ndfip2 limits inflammation. Supporting this, using a T cell transfer model of colitis, we found that transfer of doubly deficient T cells caused more severe disease compared to transfer of Ndfip1-/- T cells. These data indicate that Ndfip2 negatively regulates effector cell function following activation. We have now tested the effects of Ndfip2 deficiency on distinct cellular subsets in models of both acute and chronic inflammatory bowel disease. These studies suggest that Ndfip1 and Ndfip2 are pleiotropic modulators of inflammation.
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Chen, An, Beixue Gao, Jingping Zhang, Tamara McEwen, Shui Q. Ye, Donna Zhang, and Deyu Fang. "The HECT-Type E3 Ubiquitin Ligase AIP2 Inhibits Activation-Induced T-Cell Death by Catalyzing EGR2 Ubiquitination." Molecular and Cellular Biology 29, no. 19 (August 3, 2009): 5348–56. http://dx.doi.org/10.1128/mcb.00407-09.
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ABSTRACT E3 ubiquitin ligases, which target specific molecules for proteolytic destruction, have emerged as key regulators of immune functions. Several E3 ubiquitin ligases, including c-Cbl, Cbl-b, GRAIL, Itch, and Nedd4, have been shown to negatively regulate T-cell activation. Here, we report that the HECT-type E3 ligase AIP2 positively regulates T-cell activation. Ectopic expression of AIP2 in mouse primary T cells enhances their proliferation and interleukin-2 production by suppressing the apoptosis of T cells. AIP2 interacts with and promotes ubiquitin-mediated degradation of EGR2, a zinc finger transcription factor that has been found to regulate Fas ligand (FasL) expression during activation-induced T-cell death. Suppression of AIP2 expression by small RNA interference upregulates EGR2, inhibits EGR2 ubiquitination and FasL expression, and enhances the apoptosis of T cells. Therefore, AIP2 regulates activation-induced T-cell death by suppressing EGR2-mediated FasL expression via the ubiquitin pathway.
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Fang, Deyu, An Chen, and Sang-Myeong Lee. "Inhibition of activation-induced T cell death by AIP2-mediated ubiquitination of EGR2 (35.20)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 35.20. http://dx.doi.org/10.4049/jimmunol.182.supp.35.20.
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Abstract E3 ubiquitin ligases, which target specific molecules for proteolytic destruction, have emerged as key regulators of immune functions. Several E3 ubiquitin ligases, including c-Cbl, Cbl-b, GRAIL, Itch, and Nedd4, have been shown to negatively regulate T-cell activation. Here we report that the HECT-type E3 ligase, AIP2, positively regulates T-cell activation. Ectopic expression of AIP2 in mouse primary T cells enhances their proliferation and IL-2 production by suppressing apoptosis of T cells. AIP2 interacts with and promotes ubiquitin-mediated degradation of EGR2, a zinc finger transcription factor that has been found to regulate Fas ligand (FasL) expression during activation-induced T cell death. Suppression of AIP2 expression by small RNA interference upregulates EGR2 and FasL expression and enhances the apoptosis of T cells. Therefore, AIP2 regulates activation-induced T cell death by suppressing EGR2-mediated FasL expression via the ubiquitin pathway.
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Yao, Weiyi, Zelin Shan, Aihong Gu, Minjie Fu, Zhifeng Shi, and Wenyu Wen. "WW domain–mediated regulation and activation of E3 ubiquitin ligase Suppressor of Deltex." Journal of Biological Chemistry 293, no. 43 (September 13, 2018): 16697–708. http://dx.doi.org/10.1074/jbc.ra118.003781.
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The Nedd4 family E3 ligases Itch and WWP1/2 play crucial roles in the regulation of cell cycle progression and apoptosis and are closely correlated with cancer development and metastasis. It has been recently shown that the ligase activities of Itch and WWP1/2 are tightly regulated, with the HECT domain sequestered intramolecularly by a linker region connecting WW2 and WW3. Here, we show that a similar autoinhibitory mechanism is utilized by the Drosophila ortholog of Itch and WWP1/2, Suppressor of Deltex (Su(dx)). We show that Su(dx) adopts an inactive steady state with the WW domain region interacting with the HECT domain. We demonstrate that both the linker and preceding WW2 are required for the efficient binding and regulation of Su(dx) HECT. Recruiting the multiple-PY motif–containing adaptor dNdfip via WW domains relieves the inhibitory state of Su(dx) and leads to substrate (e.g. Notch) ubiquitination. Our study demonstrates an evolutionarily conservative mechanism governing the regulation and activation of some Nedd4 family E3 ligases. Our results also suggest a dual regulatory mechanism for specific Notch down-regulation via dNdfip–Su(dx)–mediated Notch ubiquitination.
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Xu, Da, Haoxun Wang, Carol Gardner, Zui Pan, Ping L. Zhang, Jinghui Zhang, and Guofeng You. "The role of Nedd4-1 WW domains in binding and regulating human organic anion transporter 1." American Journal of Physiology-Renal Physiology 311, no. 2 (August 1, 2016): F320—F329. http://dx.doi.org/10.1152/ajprenal.00153.2016.
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Human organic anion transporter 1 (hOAT1), expressed at the basolateral membrane of kidney proximal tubule cells, mediates the active renal secretion of a diverse array of clinically important drugs, including anti-human immunodeficiency virus therapeutics, antitumor drugs, antibiotics, antihypertensives, and anti-inflammatories. We have previously demonstrated that posttranslational modification of hOAT1 by ubiquitination is an important mechanism for the regulation of this transporter. The present study aimed at identifying the ubiquitin ligase for hOAT1 and its mechanism of action. We showed that overexpression of neural precursor cell expressed, developmentally downregulated (Nedd)4-1, an E3 ubiquitin ligase, enhanced hOAT1 ubiquitination, decreased hOAT1 expression at the cell surface, and inhibited hOAT1 transport activity. In contrast, overexpression of the ubiquitin ligase-dead mutant Nedd4-1/C867S was without effects on hOAT1. Furthermore, knockdown of endogenously expressed Nedd4-1 by Nedd4-1-specific small interfering RNA reduced hOAT1 ubiquitination. Immunoprecipitation experiments in cultured cells and rat kidney slices and immunofluorescence experiments in rat kidney slices showed that there was a physical interaction between OAT1 and Nedd4-1. Nedd4-1 contains four protein-protein interacting WW domains. When these WW domains were inactivated by mutating two amino acid residues in each of the four WW domains (Mut-WW1: V210W/H212G, Mut-WW2: V367W/H369G, Mut-WW3: I440W/H442G, and Mut-WW4: I492W/H494G, respectively), only Mut-WW2 and Mut-WW3 significantly lost their ability to bind and to ubiquitinate hOAT1. As a result, Mut-WW2 and Mut-WW3 were unable to suppress hOAT1-mediated transport as effectively as wild-type Nedd4-1. In conclusion, this is the first demonstration that Nedd4-1 regulates hOAT1 ubiquitination, expression, and transport activity through its WW2 and WW3 domains.
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Kawakami, T. "NEDD8 recruits E2-ubiquitin to SCF E3 ligase." EMBO Journal 20, no. 15 (August 1, 2001): 4003–12. http://dx.doi.org/10.1093/emboj/20.15.4003.
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Han, Sang-oh, Kunhong Xiao, Jihee Kim, Jiao-Hui Wu, James W. Wisler, Nobuhiro Nakamura, Neil J. Freedman, and Sudha K. Shenoy. "MARCH2 promotes endocytosis and lysosomal sorting of carvedilol-bound β2-adrenergic receptors." Journal of Cell Biology 199, no. 5 (November 19, 2012): 817–30. http://dx.doi.org/10.1083/jcb.201208192.
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Lysosomal degradation of ubiquitinated β2-adrenergic receptors (β2ARs) serves as a major mechanism of long-term desensitization in response to prolonged agonist stimulation. Surprisingly, the βAR antagonist carvedilol also induced ubiquitination and lysosomal trafficking of both endogenously expressed β2ARs in vascular smooth muscle cells (VSMCs) and overexpressed Flag-β2ARs in HEK-293 cells. Carvedilol prevented β2AR recycling, blocked recruitment of Nedd4 E3 ligase, and promoted the dissociation of the deubiquitinases USP20 and USP33. Using proteomics approaches (liquid chromatography–tandem mass spectrometry), we identified that the E3 ligase MARCH2 interacted with carvedilol-bound β2AR. The association of MARCH2 with internalized β2ARs was stabilized by carvedilol and did not involve β-arrestin. Small interfering RNA–mediated down-regulation of MARCH2 ablated carvedilol-induced ubiquitination, endocytosis, and degradation of endogenous β2ARs in VSMCs. These findings strongly suggest that specific ligands recruit distinct E3 ligase machineries to activated cell surface receptors and direct their intracellular itinerary. In response to β blocker therapy with carvedilol, MARCH2 E3 ligase activity regulates cell surface β2AR expression and, consequently, its signaling.
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Vogiatzis, Stefania, Michele Celestino, Marta Trevisan, Gloria Magro, Claudia Del Vecchio, Deran Erdengiz, Giorgio Palù, Cristina Parolin, Kathleen Maguire-Zeiss, and Arianna Calistri. "Lentiviral Vectors Expressing Chimeric NEDD4 Ubiquitin Ligases: An Innovative Approach for Interfering with Alpha-Synuclein Accumulation." Cells 10, no. 11 (November 21, 2021): 3256. http://dx.doi.org/10.3390/cells10113256.
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One of the main pathological features of Parkinson’s disease (PD) is a diffuse accumulation of alpha-synuclein (aS) aggregates in neurons. The NEDD4 E3 Ub ligase promotes aS degradation by the endosomal–lysosomal route. Interestingly, NEDD4, as well as being a small molecule able to trigger its functions, is protective against human aS toxicity in evolutionary distant models. While pharmacological activation of E3 enzymes is not easy to achieve, their flexibility and the lack of “consensus” motifs for Ub-conjugation allow the development of engineered Ub-ligases, able to target proteins of interest. We developed lentiviral vectors, encoding well-characterized anti-human aS scFvs fused in frame to the NEDD4 catalytic domain (ubiquibodies), in order to target ubiquitinate aS. We demonstrate that, while all generated ubiquibodies bind to and ubiquitinate aS, the one directed against the non-amyloid component (NAC) of aS (Nac32HECT) affects aS’s intracellular levels. Furthermore, Nac32HECT expression partially rescues aS’s overexpression or mutation toxicity in neural stem cells. Overall, our data suggest that ubiquibodies, and Nac32HECT in particular, represent a valid platform for interfering with the effects of aS’s accumulation and aggregation in neurons.
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Batuello, Christopher N., Paula M. Hauck, Jaimie M. Gendron, Jason A. Lehman, and Lindsey D. Mayo. "Src phosphorylation converts Mdm2 from a ubiquitinating to a neddylating E3 ligase." Proceedings of the National Academy of Sciences 112, no. 6 (January 26, 2015): 1749–54. http://dx.doi.org/10.1073/pnas.1416656112.
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Murine double minute-2 protein (Mdm2) is a multifaceted phosphorylated protein that plays a role in regulating numerous proteins including the tumor suppressor protein p53. Mdm2 binds to and is involved in conjugating either ubiquitin or Nedd8 (Neural precursor cell expressed, developmentally down-regulated 8) to p53. Although regulation of the E3 ubiquitin activity of Mdm2 has been investigated, regulation of the neddylating activity of Mdm2 remains to be defined. Here we show that activated c-Src kinase phosphorylates Y281 and Y302 of Mdm2, resulting in an increase in Mdm2 stability and its association with Ubc12, the E2 enzyme of the neddylating complex. Mdm2-dependent Nedd8 conjugation of p53 results in transcriptionally inactive p53, a process that is reversed with a small molecule inhibitor to either Src or Ubc12. Thus, our studies reveal how Mdm2 may neutralize and elevate p53 in actively proliferating cells and also provides a rationale for using therapies that target the Nedd8 pathway in wild-type p53 tumors.
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Santonico, Elena. "Old and New Concepts in Ubiquitin and NEDD8 Recognition." Biomolecules 10, no. 4 (April 7, 2020): 566. http://dx.doi.org/10.3390/biom10040566.
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Post-translational modifications by ubiquitin and ubiquitin-like proteins (Ubls) have known roles in a myriad of cellular processes. Ubiquitin- and Ubl-binding domains transmit the information conferred by these post-translational modifications by recognizing functional surfaces and, when present, different chain structures. Numerous domains binding to ubiquitin have been characterized and their structures solved. Analogously, motifs selectively interacting with SUMO (small ubiquitin-like modifier) have been identified in several proteins and their role in SUMO-dependent processes investigated. On the other hand, proteins that specifically recognize other Ubl modifications are known only in a few cases. The high sequence identity between NEDD8 and ubiquitin has made the identification of specific NEDD8-binding domains further complicated due to the promiscuity in the recognition by several ubiquitin-binding domains. Two evolutionarily related domains, called CUBAN (cullin-binding domain associating with NEDD8) and CoCUN (cousin of CUBAN), have been recently described. The CUBAN binds monomeric NEDD8 and neddylated cullins, but it also interacts with di-ubiquitin chains. Conversely, the CoCUN domain only binds ubiquitin. CUBAN and CoCUN provide an intriguing example of how nature solved the issue of promiscuity versus selectivity in the recognition of these two highly related molecules. The structural information available to date suggests that the ancestor of CUBAN and CoCUN was a three-helix bundle domain that diversified in KHNYN (KH and NYN domain-containing) and N4BP1 (NEDD4-binding protein-1) by acquiring different features. Indeed, these domains diverged towards two recognition modes, that recall respectively the electrostatic interaction utilized by the E3-ligase RBX1/2 in the interaction with NEDD8, and the hydrophobic features described in the recognition of ubiquitin by CUE (coupling ubiquitin conjugation to ER degradation) domains. Intriguingly, CUBAN and CoCUN domains are only found in KHNYN and N4BP1, respectively, both proteins belonging to the PRORP family whose members are characterized by the combination of protein modules involved in RNA metabolism with domains mediating ubiquitin/NEDD8 recognition. This review recapitulates the current knowledge and recent findings of CUBAN and CoCUN domains and the proteins containing them.
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Fontan, Lorena, John Hatcher, David Scott, Qi Qiao, Ilkay Us, Guangyan Du, Matthew Durant, et al. "Chemically Induced Degradation of MALT1 to Treat B-Cell Lymphomas." Blood 134, Supplement_1 (November 13, 2019): 2073. http://dx.doi.org/10.1182/blood-2019-130666.
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MALT1 is a protease and scaffold protein involved in signal transduction to NF-κB downstream of several receptors including B-cell (BCR) and T-cell receptors (TCR). MALT1 is aberrantly activated in ABC DLBCL by mutations in upstream genes in the BCR and TLR pathways (CD79A/B, CARD11, MYD88) and is critical for proliferation and survival. Recent studies by our lab, and others, identified inhibitors of MALT1 protease activity that revealed MALT1 is therapeutically targetable in ABC DLBCL. MALT1 is also essential for CLL, MCL and certain solid tumors (most notably lung cancer and glioblastoma). A first-in-man clinical trial recently started to evaluate MALT1 protease inhibition in B-cell non-Hodgkin's lymphomas. However, chronic inactivation of MALT1 protease activity suppressed T regulatory cells in vivo in protease dead murine models causing fast progressing autoimmune disease and death. Loss of MALT1, on the other hand, has also potent anti-tumoral effects but does not lead to autoimmunity in murine models. These findings prompted us to study alternative MALT1 targeting therapeutic approaches aimed to target its scaffolding activity. We have developed a series of proteolytic targeting chimera (PROTAC) compounds against MALT1. PROTACs are bifunctional compounds that induce selective proteolysis by targeting proteins of interest to E3 ligases for directed proteosomal degradation. Our MALT1 PROTACs are based on an allosteric MALT1 inhibitor that binds reversibly to MALT1 and fused to a Cereblon (CRBN) binding moiety, with the intent of bringing the CRBN E3 ligase complex in close proximity of MALT1 and promoting its ubiquitination and proteasomal degradation. We performed structure-activity relationship analysis and studied: 1) three linker attachment points in the MALT1 binding moiety and evaluated their MALT1 enzymatic inhibitory activity and binding to MALT1; 2) the effect of distinct linker length and polarity in MALT1 degradation and, 3) compared the effect of Lenalidomide, Pomalidomide and CC-220, which have increasing CRBN affinities, as alternative CRBN-binding moieties. Six out of eighteen compounds presented higher than 50% MALT1 degradation at 1 μM compared to vehicle treated cells in a MALT1-dependent cell line, OCI-Ly3. The parental allosteric compound, on the other hand, did not affect MALT1 levels compared to vehicle treated cells and was used as a negative control for MALT1 degradation. Compounds that actively degraded MALT1 over 50% preserved selective killing of ABC DLBCL over GCB DLBCL, same as the parental MALT1 inhibitor. GI50 of active compounds in OCI-Ly3 was 2-6 μM while it was greater than 20 μM for the MALT1-independent cell line OCI-Ly1. We chose two of our most effective and selective compounds to validate MALT1 PROTACs mechanism of action. Unlike their parental MALT1 targeting allosteric compound, MALT1 PROTACs effectively degraded MALT1 in a CRBN-dependent manner as shown in a 293T-CRBN knockout cell line or in OCI-Ly3 cells by treatment with 1 μM MLN4924. MLN4924 inhibits NEDD8-activating enzyme which is essential for the CRBN complex to function. Notably, MALT1 PROTACs degraded MALT1 in OCI-Ly1 cells (FC=-2.5) and Raji cells (FC=-1.7), where MALT1 is inactive. MALT1 degradation by PROTACs was not affected by activation in Raji cells, since PMA/ionomycin treatment did not alter the effect of MALT1 PROTACs on MALT1 levels. Therefore, MALT1 PROTACs can degrade MALT1 independent of its activation state. Moreover, unlike MALT1 protease inhibitors, MALT1 PROTACs potently suppress NF-κB activation, which is dependent on MALT1 scaffolding activity, as assessed by WB of phopho and total IκB in ABC DLBCL cell lines. Our data shows that MALT1 PROTACs could be excellent agents for the treatment of ABC DLBCL and other lymphomas, providing an alternative to enzymatic targeting that might prove useful to avoid autoimmunity or overcome resistance mechanisms. Disclosures Gray: Gatekeeper, Syros, Petra, C4, B2S and Soltego.: Equity Ownership; Novartis, Takeda, Astellas, Taiho, Janssen, Kinogen, Voronoi, Her2llc, Deerfield and Sanofi.: Equity Ownership, Research Funding. Melnick:Constellation: Consultancy; Janssen: Research Funding; Epizyme: Consultancy.
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Xu, Da, Haoxun Wang, Qiang Zhang, and Guofeng You. "Nedd4-2 but not Nedd4-1 is critical for protein kinase C-regulated ubiquitination, expression, and transport activity of human organic anion transporter 1." American Journal of Physiology-Renal Physiology 310, no. 9 (May 1, 2016): F821—F831. http://dx.doi.org/10.1152/ajprenal.00522.2015.
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Human organic anion transporter 1 (hOAT1) expressed at the membrane of the kidney proximal tubule cells mediates the body disposition of a diverse array of clinically important drugs, including anti-HIV therapeutics, antitumor drugs, antibiotics, antihypertensives, and antiinflammatories. Therefore, understanding the regulation of hOAT1 will provide significant insights into kidney function and dysfunction. We previously established that hOAT1 transport activity is inhibited by activation of protein kinase C (PKC) through accelerating hOAT1 internalization from cell surface into intracellular endosomes and subsequent degradation. We further established that PKC-induced hOAT1 ubiquitination is an important step preceding hOAT1 internalization. In the current study, we identified two closely related E3 ubiquitin ligases, neural precursor cell expressed, developmentally downregulated 4-1 and 4-2 (Nedd4-1 and Nedd4-2), as important regulators for hOAT1: overexpression of Nedd4-1 or Nedd4-2 enhanced hOAT1 ubiquitination, reduced the hOAT1 amount at the cell surface, and suppressed hOAT1 transport activity. In further exploring the relationship among PKC, Nedd4-1, and Nedd4-2, we discovered that PKC-dependent changes in hOAT1 ubiquitination, expression, and transport activity were significantly blocked in cells transfected with the ligase-dead mutant of Nedd4-2 (Nedd4-2/C821A) or with Nedd4-2-specific siRNA to knockdown endogenous Nedd4-2 but not in cells transfected with the ligase-dead mutant of Nedd4-1 (Nedd4-1/C867S) or with Nedd4-1-specific siRNA to knockdown endogenous Nedd4-1. In conclusion, this is the first demonstration that both Nedd4-1 and Nedd4-2 are important regulators for hOAT1 ubiquitination, expression, and function. Yet they play distinct roles, as Nedd4-2 but not Nedd4-1 is a critical mediator for PKC-regulated hOAT1 ubiquitination, expression, and transport activity.
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Leclerc, Gilles M., Shuhua Zheng, Guy J. Leclerc, Joanna DeSalvo, Ronan T. Swords, and Julio C. Barredo. "The NEDD8 Activating Enzyme Inhibitor Pevonedistat Induces ER Stress/UPR-Mediated Cell Death and Rebalances Homeostasis of Pro- and Anti-Apoptotic Proteins in Favor of Cell Death in Acute Lymphoblastic Leukemia Cells." Blood 126, no. 23 (December 3, 2015): 1327. http://dx.doi.org/10.1182/blood.v126.23.1327.1327.
Full textAbstract:
Abstract Acute lymphoblastic leukemia (ALL) is the leading cause of cancer-related death in children. Most adults will die from the disease. Hence, current therapy in ALL is inadequate. We previously showed that ALL cells were differentially sensitive to agents inducing endoplasmic reticulum (ER) stress (Mol Cancer Res 2012; 10:969-978; PLoS One 2013; 8:e74420). In this regard, we investigated the anti-leukemic activity of the NEDD8-activating enzyme (NAE) inhibitor pevonedistat (MLN4924). Pevonedistat prevents neddylation of cullin-RING E3 ligases, leading to accumulation of cullin dependent substrates with anti-proliferative effects. We demonstrated that pevonedistat induced dose-dependent cell growth inhibition (IC50 between 159-300 nM) and cell death (EC50 between 317-463 nM) in both T- and B-ALL cells (cell lines and primary patient material). We found that neddylated cullin levels were significantly decreased confirming inhibition of the NEDD8 conjugation pathway by pevonedistat. Pevonedistat induced ER stress and unfolded protein response (UPR) mediated cell death in ALL cell lines and primary cells as evidenced by increased expression of UPR markers (GRP78 and CHOP), and cleaved-PARP. Mechanistically, pevonedistat caused proteotoxic/ER stress from failure to halt protein translation mediated by p-eIF2α (Ser51) de-phosphorylation via up-regulation of the PERK inhibitor p58IPK. We also observed up-regulation of mTOR/p70S6K, further increasing protein synthesis and augmenting proteotoxic/ER stress. Indeed, we demonstrated that pevonedistat induced nascent protein synthesis, and that co-treatment with protein synthesis inhibitors (rapamycin, cycloheximide) rescued ALL cells from pevonedistat induced cytotoxicity (p < 0.01 for combination treatment vs. pevonedistat alone). The observed rescue correlated with decreased UPR markers and P-p70S6K (Thr389) expression, suggesting that proteotoxic stress is a central determinant in pevonedistat-induced ALL cell death. Additional studies into the mechanism of pevonedistat-induced apoptosis revealed that homeostasis of pro- and anti-apoptotic proteins was rebalanced in favor of cell death through decreased Mcl-1 pro-survival activity, via sequestration by NOXA and BIM. Co-immunoprecipitation experiments showed that pevonedistat increased the interaction between NOXA and Mcl-1, and BIM and Mcl-1 proteins, resulting in the reduction of Mcl-1 pro-survival activity. siRNA-mediated down-regulation of NOXA and BIM expression decreased the sensitivity of ALL cells to pevonedistat, supporting the sequestration by NOXA and BIM of Mcl-1's pro-survival activity. Activation of the MEK/ERK/Mcl-1 pathway following pevonedistat-induced cell death was also noted, possibly as a compensatory mechanism. We found that pevonedistat plus a MEK inhibitor (PD98059, selumetinib) induced significant cell death compared to each drug alone (p < 0.0001), which was associated with decreased Mcl-1 expression and increased cleaved-PARP cleavage, supporting a critical role of Mcl-1 in ALL cell survival. In addition, we demonstrated synergy between pevonedistat and effective anti-leukemic agents such as dexamethasone, doxorubicin and cytarabine in ALL cell line models, with CI values of 0.17, 0.46, and 0.23, respectively. More importantly, we showed that NSG mice engrafted with human ALL cells had statistically significant increased survival when treated with pevonedistat (pevo) plus dexamethasone (dex) compared to single agent therapy (p = 0.0076 for pevo+dex vs. dex alone; p = 0.0182 pevo+dex vs. pevo alone), lending support for the use of pevonedistat as part of a multi-agent approach. Taken together, our data demonstrate that the NAE inhibitor pevonedistat alters cellular translational machinery leading to ER stress/UPR-mediated cell death, and suggest that pevonedistat may have a "priming" effect on ALL cells by altering the apoptotic threshold through modulation of Mcl-1's pro-survival activity. Disclosures No relevant conflicts of interest to declare.
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Bhandari, Deepali, Seth L. Robia, and Adriano Marchese. "The E3 Ubiquitin Ligase Atrophin Interacting Protein 4 Binds Directly To The Chemokine Receptor CXCR4 Via a Novel WW Domain-mediated Interaction." Molecular Biology of the Cell 20, no. 5 (March 2009): 1324–39. http://dx.doi.org/10.1091/mbc.e08-03-0308.
Full textAbstract:
The E3 ubiquitin ligase atrophin interacting protein 4 (AIP4) mediates ubiquitination and down-regulation of the chemokine receptor CXCR4. AIP4 belongs to the Nedd4-like homologous to E6-AP carboxy terminus domain family of E3 ubiquitin ligases, which typically bind proline-rich motifs within target proteins via the WW domains. The intracellular domains of CXCR4 lack canonical WW domain binding motifs; thus, whether AIP4 is targeted to CXCR4 directly or indirectly via an adaptor protein remains unknown. Here, we show that AIP4 can interact directly with CXCR4 via a novel noncanonical WW domain-mediated interaction involving serine residues 324 and 325 within the carboxy-terminal tail of CXCR4. These serine residues are critical for mediating agonist-promoted binding of AIP4 and subsequent ubiquitination and degradation of CXCR4. These residues are phosphorylated upon agonist activation and phosphomimetic mutants show enhanced binding to AIP4, suggesting a mechanism whereby phosphorylation mediates the interaction between CXCR4 and AIP4. Our data reveal a novel noncanonical WW domain-mediated interaction involving phosphorylated serine residues in the absence of any proline residues and suggest a novel mechanism whereby an E3 ubiquitin ligase is targeted directly to an activated G protein-coupled receptor.