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Suranjika S, Barla P, Sharma N, Dey N. A review on ubiquitin ligases: Orchestrators of plant resilience in adversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112180. [PMID: 38964613 DOI: 10.1016/j.plantsci.2024.112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Ubiquitin- proteasome system (UPS) is universally present in plants and animals, mediating many cellular processes needed for growth and development. Plants constantly defend themselves against endogenous and exogenous stimuli such as hormonal signaling, biotic stresses such as viruses, fungi, nematodes, and abiotic stresses like drought, heat, and salinity by developing complex regulatory mechanisms. Ubiquitination is a regulatory mechanism involving selective elimination and stabilization of regulatory proteins through the UPS system where E3 ligases play a central role; they can bind to the targets in a substrate-specific manner, followed by poly-ubiquitylation, and subsequent protein degradation by 26 S proteasome. Increasing evidence suggests different types of E3 ligases play important roles in plant development and stress adaptation. Herein, we summarize recent advances in understanding the regulatory roles of different E3 ligases and primarily focus on protein ubiquitination in plant-environment interactions. It also highlights the diversity and complexity of these metabolic pathways that enable plant to survive under challenging conditions. This reader-friendly review provides a comprehensive overview of E3 ligases and their substrates associated with abiotic and biotic stresses that could be utilized for future crop improvement.
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Affiliation(s)
- Sandhya Suranjika
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India; Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha, India
| | - Preeti Barla
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Namisha Sharma
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India.
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2
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Pan CR, Knutson SD, Huth SW, MacMillan DWC. µMap proximity labeling in living cells reveals stress granule disassembly mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01721-2. [PMID: 39215100 DOI: 10.1038/s41589-024-01721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Phase-separated condensates are membrane-less intracellular structures comprising dynamic protein interactions that organize essential biological processes. Understanding the composition and dynamics of these organelles advances our knowledge of cellular behaviors and disease pathologies related to granule dysregulation. In this study, we apply microenvironment mapping with a HaloTag-based platform (HaloMap) to characterize intracellular stress granule dynamics in living cells. After validating the robustness and sensitivity of this approach, we then profile the stress granule proteome throughout the formation and disassembly and under pharmacological perturbation. These experiments reveal several ubiquitin-related modulators, including the HECT (homologous to E6AP C terminus) E3 ligases ITCH and NEDD4L, as well as the ubiquitin receptor toll-interacting protein TOLLIP, as key mediators of granule disassembly. In addition, we identify an autophagy-related pathway that promotes granule clearance. Collectively, this work establishes a general photoproximity labeling approach for unraveling intracellular protein interactomes and uncovers previously unexplored regulatory mechanisms of stress granule dynamics.
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Affiliation(s)
- Chenmengxiao Roderick Pan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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3
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Pergel E, Tóth DJ, Baukál D, Veres I, Czirják G. The Ubiquitin Ligase Adaptor NDFIP1 Interacts with TRESK and Negatively Regulates the Background K + Current. Int J Mol Sci 2024; 25:8879. [PMID: 39201565 PMCID: PMC11355008 DOI: 10.3390/ijms25168879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
The TRESK (K2P18.1, KCNK18) background potassium channel is expressed in primary sensory neurons and has been reported to contribute to the regulation of pain sensations. In the present study, we examined the interaction of TRESK with NDFIP1 (Nedd4 family-interacting protein 1) in the Xenopus oocyte expression system by two-electrode voltage clamp and biochemical methods. We showed that the coexpression of NDFIP1 abolished the TRESK current under the condition where the other K+ channels were not affected. Mutations in the three PPxY motifs of NDFIP1, which are responsible for the interaction with the Nedd4 ubiquitin ligase, prevented a reduction in the TRESK current. Furthermore, the overexpression of a dominant-negative Nedd4 construct in the oocytes coexpressing TRESK with NDFIP1 partially reversed the down-modulating effect of the adaptor protein on the K+ current. The biochemical data were also consistent with the functional results. An interaction between epitope-tagged versions of TRESK and NDFIP1 was verified by co-immunoprecipitation experiments. The coexpression of NDFIP1 with TRESK induced the ubiquitination of the channel protein. Altogether, the results suggest that TRESK is directly controlled by and highly sensitive to the activation of the NDFIP1-Nedd4 system. The NDFIP1-mediated reduction in the TRESK component may induce depolarization, increase excitability, and attenuate the calcium dependence of the membrane potential by reducing the calcineurin-activated fraction in the ensemble background K+ current.
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Affiliation(s)
- Enikő Pergel
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary; (E.P.); (D.B.); (I.V.)
| | - Dániel J. Tóth
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary; (E.P.); (D.B.); (I.V.)
- HUN-REN-SU Molecular Physiology Research Group, Hungarian Research Network and Semmelweis University, 1094 Budapest, Hungary
| | - Dóra Baukál
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary; (E.P.); (D.B.); (I.V.)
| | - Irén Veres
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary; (E.P.); (D.B.); (I.V.)
| | - Gábor Czirják
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary; (E.P.); (D.B.); (I.V.)
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4
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Bolado-Carrancio A, Tapia O, Rodríguez-Rey JC. Ubiquitination Insight from Spinal Muscular Atrophy-From Pathogenesis to Therapy: A Muscle Perspective. Int J Mol Sci 2024; 25:8800. [PMID: 39201486 PMCID: PMC11354275 DOI: 10.3390/ijms25168800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/03/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most frequent causes of death in childhood. The disease's molecular basis is deletion or mutations in the SMN1 gene, which produces reduced survival motor neuron protein (SMN) levels. As a result, there is spinal motor neuron degeneration and a large increase in muscle atrophy, in which the ubiquitin-proteasome system (UPS) plays a significant role. In humans, a paralogue of SMN1, SMN2 encodes the truncated protein SMNΔ7. Structural differences between SMN and SMNΔ7 affect the interaction of the proteins with UPS and decrease the stability of the truncated protein. SMN loss affects the general ubiquitination process by lowering the levels of UBA1, one of the main enzymes in the ubiquitination process. We discuss how SMN loss affects both SMN stability and the general ubiquitination process, and how the proteins involved in ubiquitination could be used as future targets for SMA treatment.
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Affiliation(s)
- Alfonso Bolado-Carrancio
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria-and Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain;
| | - Olga Tapia
- Departamento de Ciencias Médicas Básicas, Instituto de Tecnologías Biomédicas, Universidad de la Laguna, 38200 La Laguna, Spain
| | - José C. Rodríguez-Rey
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria-and Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain;
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Jiang H, Miller BD, Viennet T, Kim H, Lee K, Arthanari H, Cole PA. Protein semisynthesis reveals plasticity in HECT E3 ubiquitin ligase mechanisms. Nat Chem 2024:10.1038/s41557-024-01576-z. [PMID: 39030419 DOI: 10.1038/s41557-024-01576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/11/2024] [Indexed: 07/21/2024]
Abstract
Lys ubiquitination is catalysed by E3 ubiquitin ligases and is central to the regulation of protein stability and cell signalling in normal and disease states. There are gaps in our understanding of E3 mechanisms, and here we use protein semisynthesis, chemical rescue, microscale thermophoresis and other biochemical approaches to dissect the role of catalytic base/acid function and conformational interconversion in HECT-domain E3 catalysis. We demonstrate that there is plasticity in the use of the terminal side chain or backbone carboxylate for proton transfer in HECT E3 ubiquitin ligase reactions, with yeast Rsp5 orthologues appearing to be possible evolutionary intermediates. We also show that the HECT-domain ubiquitin covalent intermediate appears to eject the E2 conjugating enzyme, promoting catalytic turnover. These findings provide key mechanistic insights into how protein ubiquitination occurs and provide a framework for understanding E3 functions and regulation.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bryant D Miller
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Human Biology, Sattler College, Boston, MA, USA
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Hyojeon Kim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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6
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Su Y, Ngea GLN, Wang K, Lu Y, Godana EA, Ackah M, Yang Q, Zhang H. Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38864414 DOI: 10.1111/pbi.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.
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Affiliation(s)
- Yingying Su
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Fisheries Sciences, University of Douala, Douala, Cameroon
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuchun Lu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Esa Abiso Godana
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Michael Ackah
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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7
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Blest HTW, Redmond A, Avissar J, Barker J, Bridgeman A, Fowler G, Chauveau L, Hertzog J, Vendrell I, Fischer R, Iversen MB, Jing L, Koelle DM, Paludan SR, Kessler BM, Crump CM, Rehwinkel J. HSV-1 employs UL56 to antagonize expression and function of cGAMP channels. Cell Rep 2024; 43:114122. [PMID: 38652659 DOI: 10.1016/j.celrep.2024.114122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/21/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
DNA sensing is important for antiviral immunity. The DNA sensor cGAS synthesizes 2'3'-cyclic GMP-AMP (cGAMP), a second messenger that activates STING, which induces innate immunity. cGAMP not only activates STING in the cell where it is produced but cGAMP also transfers to other cells. Transporters, channels, and pores (including SLC19A1, SLC46A2, P2X7, ABCC1, and volume-regulated anion channels (VRACs)) release cGAMP into the extracellular space and/or import cGAMP. We report that infection with multiple human viruses depletes some of these cGAMP conduits. This includes herpes simplex virus 1 (HSV-1) that targets SLC46A2, P2X7, and the VRAC subunits LRRC8A and LRRC8C for degradation. The HSV-1 protein UL56 is necessary and sufficient for these effects that are mediated at least partially by proteasomal turnover. UL56 thereby inhibits cGAMP uptake via VRAC, SLC46A2, and P2X7. Taken together, HSV-1 antagonizes intercellular cGAMP transfer. We propose that this limits innate immunity by reducing cell-to-cell communication via the immunotransmitter cGAMP.
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Affiliation(s)
- Henry T W Blest
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Alexander Redmond
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jed Avissar
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jake Barker
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Anne Bridgeman
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Gerissa Fowler
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Lise Chauveau
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marie B Iversen
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK.
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8
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Yu L, Chen Z, Wu Y, Xu M, Zhong D, Xu H, Zhu W. Unraveling role of ubiquitination in drug resistance of gynecological cancer. Am J Cancer Res 2024; 14:2523-2537. [PMID: 38859858 PMCID: PMC11162667 DOI: 10.62347/wykz9784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024] Open
Abstract
Chemotherapy is the principal treatment for advanced cancer patients. However, chemotherapeutic resistance, an important hallmark of cancer, is considered as a key impediment to effective therapy in cancer patients. Multiple signaling pathways and factors have been underscored to participate in governing drug resistance. Posttranslational modifications, including ubiquitination, glycosylation, acetylation and phosphorylation, have emerged as key players in modulating drug resistance in gynecological tumors, such as ovarian cancer, cervical cancer and endometrial cancer. In this review article, we summarize the role of ubiquitination in governing drug sensitivity in gynecological cancers. Moreover, we describe the numerous compounds that target ubiquitination in gynecological cancers to reverse chemotherapeutic resistance. In addition, we provide the future perspectives to fully elucidate the mechanisms by which ubiquitination controls drug resistance in gynecological tumors, contributing to restoring drug sensitivity. This review highlights the complex interplay between ubiquitination and drug resistance in gynecological tumors, providing novel insights into potential therapeutic targets and personalized treatment strategies to overcome the bottleneck of drug resistance.
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Affiliation(s)
- Li Yu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Zheling Chen
- Cancer Center, Department of Medical Oncology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Ying Wu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Meiliang Xu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Difei Zhong
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Hongen Xu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Wei Zhu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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10
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Rong Z, Zheng K, Chen J, Jin X. The cross talk of ubiquitination and chemotherapy tolerance in colorectal cancer. J Cancer Res Clin Oncol 2024; 150:154. [PMID: 38521878 PMCID: PMC10960765 DOI: 10.1007/s00432-024-05659-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Ubiquitination, a highly adaptable post-translational modification, plays a pivotal role in maintaining cellular protein homeostasis, encompassing cancer chemoresistance-associated proteins. Recent findings have indicated a potential correlation between perturbations in the ubiquitination process and the emergence of drug resistance in CRC cancer. Consequently, numerous studies have spurred the advancement of compounds specifically designed to target ubiquitinates, offering promising prospects for cancer therapy. In this review, we highlight the role of ubiquitination enzymes associated with chemoresistance to chemotherapy via the Wnt/β-catenin signaling pathway, epithelial-mesenchymal transition (EMT), and cell cycle perturbation. In addition, we summarize the application and role of small compounds that target ubiquitination enzymes for CRC treatment, along with the significance of targeting ubiquitination enzymes as potential cancer therapies.
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Affiliation(s)
- Ze Rong
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Kaifeng Zheng
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Jun Chen
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Xiaofeng Jin
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo, 315211, China.
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11
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Li W, Wang Z. Ubiquitination Process Mediates Prostate Cancer Development and Metastasis through Multiple Mechanisms. Cell Biochem Biophys 2024; 82:77-90. [PMID: 37847340 PMCID: PMC10866789 DOI: 10.1007/s12013-023-01156-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/30/2023] [Indexed: 10/18/2023]
Abstract
Prostate cancer (PCa) is a common malignant tumor in men, when the disease progresses to the advanced stage, most patients will develop distant metastasis and develop into castration-resistant prostate cancer (CRPC), resulting in increased mortality. Ubiquitination is a widespread protein post-translational modification process in the biological world, and it plays an important role in the development and transfer of PCa. E3 ubiquitin ligase plays an important role in the specific selection and role of substrates in the process of ubiquitination ligase. This review will briefly introduce the ubiquitination process and E3 ubiquitin ligase, focus on the recently discovered multiple mechanisms by which ubiquitination affects PCa development and metastasis, and a summary of the current emerging proteolysis-targeting chimeras (PROTAC) in the treatment of PCa.
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Affiliation(s)
- Wen Li
- Department of Immuno-Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhiyu Wang
- Department of Immuno-Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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12
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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13
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Xiao Y, Liu R, Li N, Li Y, Huang X. Role of the ubiquitin-proteasome system on macrophages in the tumor microenvironment. J Cell Physiol 2024; 239:e31180. [PMID: 38219045 DOI: 10.1002/jcp.31180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
Tumor-associated macrophages (TAMs) are key components of the tumor microenvironment, and their different polarization states play multiple roles in tumors by secreting cytokines, chemokines, and so on, which are closely related to tumor development. In addition, the enrichment of TAMs is often associated with poor prognosis of tumors. Thus, targeting TAMs is a potential tumor treatment strategy, in which therapeutic approaches such as reducing TAMs numbers, remodeling TAMs phenotypes, and altering their functions are being extensively investigated. Meanwhile, the ubiquitin-proteasome system (UPS), an important mechanism of protein hydrolysis in eukaryotic cells, participates in cellular processes by regulating the activity and stability of key proteins. Interestingly, UPS plays a dual role in the process of tumor development, and its role in TAMs deserve to be investigated in depth. This review builds on this foundation to further explore the multiple roles of UPS on TAMs and identifies a promising approach to treat tumors by targeting TAMs with UPS.
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Affiliation(s)
- Yue Xiao
- First School of Clinical Medicine, Nanchang University, Nanchang, China
| | - Ruiqian Liu
- School of Future Technology, Nanchang University, Nanchang, China
| | - Na Li
- School of Future Technology, Nanchang University, Nanchang, China
| | - Yong Li
- Department of Anesthesiology, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuan Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
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14
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Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Pérez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA. Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat Chem Biol 2024; 20:190-200. [PMID: 37620400 PMCID: PMC10830417 DOI: 10.1038/s41589-023-01414-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
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Affiliation(s)
- Laura A Hehl
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David A Pérez Berrocal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Brenda A Schulman
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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15
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Tessier TM, Chowdhury A, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU, Zhang W. Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Sci 2024; 33:e4885. [PMID: 38147466 PMCID: PMC10823456 DOI: 10.1002/pro.4885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Abstract
Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross-reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein-based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2-E3 protein interaction interface.
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Affiliation(s)
- Tanner M. Tessier
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Arvid Chowdhury
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Zane Stekel
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Julia Fux
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Nick Jarvik
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Jacky Chung
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Igor Kurinov
- NE‐CAT, Department of Chemistry and Chemical BiologyCornell UniversityArgonneIllinoisUSA
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoOntarioCanada
| | - Sachdev S. Sidhu
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Alex U. Singer
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Wei Zhang
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
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16
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Lee KT, Pranoto IKA, Kim SY, Choi HJ, To NB, Chae H, Lee JY, Kim JE, Kwon YV, Nam JW. Comparative interactome analysis of α-arrestin families in human and Drosophila. eLife 2024; 12:RP88328. [PMID: 38270169 PMCID: PMC10945707 DOI: 10.7554/elife.88328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
The α-arrestins form a large family of evolutionally conserved modulators that control diverse signaling pathways, including both G-protein-coupled receptor (GPCR)-mediated and non-GPCR-mediated pathways, across eukaryotes. However, unlike β-arrestins, only a few α-arrestin targets and functions have been characterized. Here, using affinity purification and mass spectrometry, we constructed interactomes for 6 human and 12 Drosophila α-arrestins. The resulting high-confidence interactomes comprised 307 and 467 prey proteins in human and Drosophila, respectively. A comparative analysis of these interactomes predicted not only conserved binding partners, such as motor proteins, proteases, ubiquitin ligases, RNA splicing factors, and GTPase-activating proteins, but also those specific to mammals, such as histone modifiers and the subunits of V-type ATPase. Given the manifestation of the interaction between the human α-arrestin, TXNIP, and the histone-modifying enzymes, including HDAC2, we undertook a global analysis of transcription signals and chromatin structures that were affected by TXNIP knockdown. We found that TXNIP activated targets by blocking HDAC2 recruitment to targets, a result that was validated by chromatin immunoprecipitation assays. Additionally, the interactome for an uncharacterized human α-arrestin ARRDC5 uncovered multiple components in the V-type ATPase, which plays a key role in bone resorption by osteoclasts. Our study presents conserved and species-specific protein-protein interaction maps for α-arrestins, which provide a valuable resource for interrogating their cellular functions for both basic and clinical research.
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Affiliation(s)
- Kyung-Tae Lee
- Department of Life Science, College of Natural Sciences, Hanyang UniversitySeoulRepublic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang UniversitySeoulRepublic of Korea
| | - Inez KA Pranoto
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Soon-Young Kim
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Hee-Joo Choi
- Bio-BigData Center, Hanyang Institute for Bioscience and Biotechnology, Hanyang UniversitySeoulRepublic of Korea
- Department of Pathology, College of Medicine, Hanyang UniversitySeoulRepublic of Korea
- Hanyang Biomedical Research Institute, Hanyang UniversitySeoulRepublic of Korea
| | - Ngoc Bao To
- Department of Life Science, College of Natural Sciences, Hanyang UniversitySeoulRepublic of Korea
| | - Hansong Chae
- Department of Life Science, College of Natural Sciences, Hanyang UniversitySeoulRepublic of Korea
| | - Jeong-Yeon Lee
- Bio-BigData Center, Hanyang Institute for Bioscience and Biotechnology, Hanyang UniversitySeoulRepublic of Korea
- Department of Pathology, College of Medicine, Hanyang UniversitySeoulRepublic of Korea
| | - Jung-Eun Kim
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Young V Kwon
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang UniversitySeoulRepublic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang UniversitySeoulRepublic of Korea
- Bio-BigData Center, Hanyang Institute for Bioscience and Biotechnology, Hanyang UniversitySeoulRepublic of Korea
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17
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Basu B, Kal S, Karmakar S, Basu M, Ghosh MK. E3 ubiquitin ligases in lung cancer: Emerging insights and therapeutic opportunities. Life Sci 2024; 336:122333. [PMID: 38061537 DOI: 10.1016/j.lfs.2023.122333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
Aim In this review, we have attempted to provide the readers with an updated account of the role of a family of proteins known as E3 ligases in different aspects of lung cancer progression, along with insights into the deregulation of expression of these proteins during lung cancer. A detailed account of the therapeutic strategies involving E3 ligases that have been developed or currently under development has also been provided in this review. MATERIALS AND METHODS: The review article employs extensive literature search, along with differential gene expression analysis of lung cancer associated E3 ligases using the DESeq2 package in R, and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/). Protein expression analysis of CPTAC lung cancer samples was carried out using the UALCAN webtool (https://ualcan.path.uab.edu/index.html). Assessment of patient overall survival (OS) in response to high and low expression of selected E3 ligases was performed using the online Kaplan-Meier plotter (https://kmplot.com/analysis/index.php?p=background). KEY FINDINGS: SIGNIFICANCE: The review provides an in-depth understanding of the role of E3 ligases in lung cancer progression and an up-to-date account of the different therapeutic strategies targeting oncogenic E3 ligases for improved lung cancer management.
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Affiliation(s)
- Bhaskar Basu
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Satadeepa Kal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhajit Karmakar
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas, PIN -743372, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
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18
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Jin J, He J, Li X, Ni X, Jin X. The role of ubiquitination and deubiquitination in PI3K/AKT/mTOR pathway: A potential target for cancer therapy. Gene 2023; 889:147807. [PMID: 37722609 DOI: 10.1016/j.gene.2023.147807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
The PI3K/AKT/mTOR pathway controls key cellular processes, including proliferation and tumor progression, and abnormally high activation of this pathway is a hallmark in human cancers. The post-translational modification, such as Ubiquitination and deubiquitination, fine-tuning the protein level and the activity of members in this pathway play a pivotal role in maintaining normal physiological process. Emerging evidence show that the unbalanced ubiquitination/deubiquitination modification leads to human diseases via PI3K/AKT/mTOR pathway. Therefore, a comprehensive understanding of the ubiquitination/deubiquitination regulation of PI3K/AKT/mTOR pathway may be helpful to uncover the underlying mechanism and improve the potential treatment of cancer via targeting this pathway. Herein, we summarize the latest research progress of ubiquitination and deubiquitination of PI3K/AKT/mTOR pathway, systematically discuss the associated crosstalk between them, as well as focus the clinical transformation via targeting ubiquitination process.
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Affiliation(s)
- Jiabei Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jian He
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xinming Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaoqi Ni
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China.
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19
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Zhou Z, Zheng K, Zhou S, Yang Y, Chen J, Jin X. E3 ubiquitin ligases in nasopharyngeal carcinoma and implications for therapies. J Mol Med (Berl) 2023; 101:1543-1565. [PMID: 37796337 DOI: 10.1007/s00109-023-02376-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most common squamous cell carcinomas of the head and neck, and Epstein-Barr virus (EBV) infection is one of the pathogenic factors involved in the oncogenetic development and progression of NPC. E3 ligases, which are key members of the ubiquitin proteasome system (UPS), specifically recognize various oncogenic factors and tumor suppressors and contribute to determining their fate through ubiquitination. Several studies have demonstrated that E3 ligases are aberrantly expressed and mutated in NPC and that these changes are closely associated with the occurrence and progression of NPC. Herein, we aim to thoroughly review the specific action mechanisms by which E3 ligases participate in NPC signaling pathways and discuss their functional relationship with EBV. Moreover, we describe the current progress in and limitations for targeted therapies against E3 ligases in NPC. KEY MESSAGES: • E3 ubiquitin ligases, as members of the UPS system, determine the fate of their substrates and may act either as oncogenic or anti-tumorigenic factors in NPC. • Mutations or dysregulated expression of E3 ubiquitin ligases is closely related to the occurrence, development, and therapeutic sensitivity of NPC, as they play important roles in several signaling pathways affected by EBV infection. • As promising therapeutic targets, E3 ligases may open new avenues for treatment and for improving the prognosis of NPC patients.
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Affiliation(s)
- Zijian Zhou
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Kaifeng Zheng
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Shao Zhou
- Department of Otolaryngology-Head and Neck Surgery, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Youxiong Yang
- Department of Otolaryngology-Head and Neck Surgery, Ningbo Yinzhou Second Hospital, Ningbo, 315199, China.
| | - Jun Chen
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Xiaofeng Jin
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center of Ningbo University, Ningbo, 315211, China.
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20
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Chuang KF, Wang CH, Chen HK, Lin YY, Lin CH, Lin YC, Shih CP, Kuo CY, Chen YC, Chen HC. GRAIL gene knockout mice protect against aging-related and noise-induced hearing loss. J Chin Med Assoc 2023; 86:1101-1108. [PMID: 37820291 DOI: 10.1097/jcma.0000000000001005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Hearing loss is a global health issue and its etiopathologies involve complex molecular pathways. The ubiquitin-proteasome system has been reported to be associated with cochlear development and hearing loss. The gene related to anergy in lymphocytes ( GRAIL ), as an E3 ubiquitin ligase, has not, as yet, been examined in aging-related and noise-induced hearing loss mice models. METHODS This study used wild-type (WT) and GRAIL knockout (KO) mice to examine cochlear hair cells and synaptic ribbons using immunofluorescence staining. The hearing in WT and KO mice was detected using auditory brainstem response. Gene expression patterns were compared using RNA-sequencing to identify potential targets during the pathogenesis of noise-induced hearing loss in WT and KO mice. RESULTS At the 12-month follow-up, GRAIL KO mice had significantly less elevation in threshold level and immunofluorescence staining showed less loss of outer hair cells and synaptic ribbons in the hook region compared with GRAIL WT mice. At days 1, 14, and 28 after noise exposure, GRAIL KO mice had significantly less elevation in threshold level than WT mice. After noise exposure, GRAIL KO mice showed less loss of outer hair cells in the cochlear hook and basal regions compared with WT mice. Moreover, immunofluorescence staining showed less loss of synaptic ribbons in the hook regions of GRAIL KO mice than of WT mice. RNA-seq analysis results showed significant differences in C-C motif chemokine ligand 19 ( CCL19 ), C-C motif chemokine ligand 21 ( CCL21 ), interleukin 25 ( IL25 ), glutathione peroxidase 6 ( GPX6 ), and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 1 ( NOX1 ) genes after noise exposure. CONCLUSION The present data demonstrated that GRAIL deficiency protects against aging-related and noise-induced hearing loss. The mechanism involved needs to be further clarified from the potential association with synaptic modulation, inflammation, and oxidative stress.
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Affiliation(s)
- Kai-Fen Chuang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
- Division of Otolaryngology, Taipei Veterans General Hospital, Taoyuan Branch, Taoyuan, Taiwan
| | - Hang-Kang Chen
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yuan-Yung Lin
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chia-Hsin Lin
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yi-Chun Lin
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cheng-Ping Shih
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chao-Yin Kuo
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ying-Chuan Chen
- Department of Physiology & Biophysics, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsin-Chien Chen
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
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21
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Park HB, Baek KH. Current and future directions of USP7 interactome in cancer study. Biochim Biophys Acta Rev Cancer 2023; 1878:188992. [PMID: 37775071 DOI: 10.1016/j.bbcan.2023.188992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The ubiquitin-proteasome system (UPS) is an essential protein quality controller for regulating protein homeostasis and autophagy. Ubiquitination is a protein modification process that involves the binding of one or more ubiquitins to substrates through a series of enzymatic processes. These include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Conversely, deubiquitination is a reverse process that removes ubiquitin from substrates via deubiquitinating enzymes (DUBs). Dysregulation of ubiquitination-related enzymes can lead to various human diseases, including cancer, through the modulation of protein ubiquitination. The most structurally and functionally studied DUB is the ubiquitin-specific protease 7 (USP7). Both the TRAF and UBL domains of USP7 are known to bind to the [P/A/E]-X-X-S or K-X-X-X-K motif of substrates. USP7 has been shown to be involved in cancer pathogenesis by binding with numerous substrates. Recently, a novel substrate of USP7 was discovered through a systemic analysis of its binding motif. This review summarizes the currently discovered substrates and cellular functions of USP7 in cancer and suggests putative substrates of USP7 through a comprehensive systemic analysis.
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Affiliation(s)
- Hong-Beom Park
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea; International Ubiquitin Center(,) CHA University, Gyeonggi-Do 13488, Republic of Korea.
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Tim B, Kouznetsova VL, Kesari S, Tsigelny IF. Targeting of insulin receptor endocytosis as a treatment to insulin resistance. J Diabetes Complications 2023; 37:108615. [PMID: 37788593 DOI: 10.1016/j.jdiacomp.2023.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/02/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Insulin resistance is the decreased effectiveness of insulin receptor function during signaling of glucose uptake. Insulin receptors are regulated by endocytosis, a process that removes receptors from the cell surface to be marked for degradation or for re-use. OBJECTIVES Our goal was to discover insulin-resistance-related genes that play key roles in endocytosis which could serve as potential biological targets to enhance insulin sensitivity. METHODS The gene mutations related to insulin resistance were elucidated from ClinVar. These were used as the seed set. Using the GeneFriends program, the genes associated with this set were elucidated and used as an enriched set for the next step. The enriched gene set network was visualized by Cytoscape. After that, using the VisANT program, the most significant cluster of genes was identified. With the help of the DAVID program, the most important KEGG pathway corresponding to the gene cluster and insulin resistance was found. Eleven genes part of the KEGG endocytosis pathway were identified. Finally, using the ChEA3 program, seven transcription factors managing these genes were defined. RESULTS Thirty-two genes of pathogenic significance in insulin resistance were elucidated, and then co-expression data for these genes were utilized. These genes were organized into clusters, one of which was singled out for its high node count of 58 genes and low p-value (p = 4.117 × 10-7). DAVID Pathways, a functional annotation tool, helped identify a set of 11 genes from a single cluster associated with the endocytosis pathway related to insulin resistance. These genes (AMPH, BIN1, CBL, DNM1, DNM2, DNM3, ITCH, SH3GL1, SH3GL2, SH3GL3, and SH3KBP1) are all involved in either clathrin-mediated endocytosis of the insulin receptor (IR) or clathrin-independent endocytosis of insulin-resistance-related G protein-coupled receptors (GPCR). They represent prime therapeutic targets to improve insulin sensitivity through modulation of transmembrane cell signaling. Using the ChEA3 database, we also found seven transcription factors (REST, MYPOP, CAMTA2, MYT1L, ZBTB18, NKX6-2, and CXXC5) that control the expression of these 11 genes. Inhibiting these key transcription factors would be another strategy to downregulate endocytosis. CONCLUSION We believe that delaying removal of insulin receptors from the cell surface would prolong signaling of glucose uptake and counteract the symptoms of insulin resistance.
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Affiliation(s)
- Bryce Tim
- IUL Science Program, San Diego, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, CA, USA; CureScience Institute, San Diego, CA, USA; BiAna, La Jolla, CA, USA
| | | | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, CA, USA; Department of Neurosciences, University of California, San Diego, CA, USA; CureScience Institute, San Diego, CA, USA; BiAna, La Jolla, CA, USA.
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23
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Jeong Y, Oh AR, Jung YH, Gi H, Kim YU, Kim K. Targeting E3 ubiquitin ligases and their adaptors as a therapeutic strategy for metabolic diseases. Exp Mol Med 2023; 55:2097-2104. [PMID: 37779139 PMCID: PMC10618535 DOI: 10.1038/s12276-023-01087-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 10/03/2023] Open
Abstract
Posttranslational modification of proteins via ubiquitination determines their activation, translocation, dysregulation, or degradation. This process targets a large number of cellular proteins, affecting all biological pathways involved in the cell cycle, development, growth, and differentiation. Thus, aberrant regulation of ubiquitination is likely associated with several diseases, including various types of metabolic diseases. Among the ubiquitin enzymes, E3 ubiquitin ligases are regarded as the most influential ubiquitin enzymes due to their ability to selectively bind and recruit target substrates for ubiquitination. Continued research on the regulatory mechanisms of E3 ligases and their adaptors in metabolic diseases will further stimulate the discovery of new targets and accelerate the development of therapeutic options for metabolic diseases. In this review, based on recent discoveries, we summarize new insights into the roles of E3 ubiquitin ligases and their adaptors in the pathogenesis of metabolic diseases by highlighting recent evidence obtained in both human and animal model studies.
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Affiliation(s)
- Yelin Jeong
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Ah-Reum Oh
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Young Hoon Jung
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - HyunJoon Gi
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Young Un Kim
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - KyeongJin Kim
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea.
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea.
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea.
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24
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Teafatiller T, Perez O, Kitazawa M, Agrawal A, Subramanian VS. Nedd4-1 regulates human sodium-dependent vitamin C transporter-2 functional expression in neuronal and epithelial cells. J Nutr Biochem 2023; 120:109413. [PMID: 37423323 DOI: 10.1016/j.jnutbio.2023.109413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
The ubiquitin-proteasomal pathway regulates the functional expression of many membrane transporters in a variety of cellular systems. Nothing is currently known about the role of ubiquitin E3 ligase, neural precursor cell-expressed developmentally down-regulated gene 4 (Nedd4-1) and the proteasomal degradation pathway in regulating human vitamin C transporter-2 (hSVCT2) in neuronal cells. hSVCT2 mediates the uptake of ascorbic acid (AA) and is the predominantly expressed vitamin C transporter isoform in neuronal systems. Therefore, we addressed this knowledge gap in our study. Analysis of mRNA revealed markedly higher expression of Nedd4-1 in neuronal samples than that of Nedd4-2. Interestingly, Nedd4-1 expression in the hippocampus was higher in patients with Alzheimer's disease (AD) and age-dependently increased in the J20 mouse model of AD. The interaction of Nedd4-1 and hSVCT2 was confirmed by coimmunoprecipitation and colocalization. While the coexpression of Nedd4-1 with hSVCT2 displayed a significant decrease in AA uptake, siRNA-mediated knockdown of Nedd4-1 expression up-regulated the AA uptake. Further, we mutated a classical Nedd4 protein interacting motif ("PPXY") within the hSVCT2 polypeptide and observed markedly decreased AA uptake due to the intracellular localization of the mutated hSVCT2. Also, we determined the role of the proteasomal degradation pathway in hSVCT2 functional expression in SH-SY5Y cells and the results indicated that the proteasomal inhibitor (MG132) significantly up-regulated the AA uptake and hSVCT2 protein expression level. Taken together, our findings show that the regulation of hSVCT2 functional expression is at least partly mediated by the Nedd4-1 dependent ubiquitination and proteasomal pathways.
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Affiliation(s)
- Trevor Teafatiller
- Department of Medicine, University of California, Irvine, California, USA
| | - Oasis Perez
- Department of Medicine, University of California, Irvine, California, USA
| | - Masashi Kitazawa
- Department of Environmental and Occupational Health, University of California, Irvine, California, USA
| | - Anshu Agrawal
- Department of Medicine, University of California, Irvine, California, USA
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25
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Yong D, Green SR, Ghiabi P, Santhakumar V, Vedadi M. Discovery of Nedd4 auto-ubiquitination inhibitors. Sci Rep 2023; 13:16057. [PMID: 37749144 PMCID: PMC10520017 DOI: 10.1038/s41598-023-42997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
E3 ubiquitin ligases are critical to the protein degradation pathway by catalyzing the final step in protein ubiquitination by mediating ubiquitin transfer from E2 enzymes to target proteins. Nedd4 is a HECT domain-containing E3 ubiquitin ligase with a wide range of protein targets, the dysregulation of which has been implicated in myriad pathologies, including cancer and Parkinson's disease. Towards the discovery of compounds disrupting the auto-ubiquitination activity of Nedd4, we developed and optimized a TR-FRET assay for high-throughput screening. Through selective screening of a library of potentially covalent compounds, compounds 25 and 81 demonstrated apparent IC50 values of 52 µM and 31 µM, respectively. Tandem mass spectrometry (MS/MS) analysis confirmed that 25 and 81 were covalently bound to Nedd4 cysteine residues (Cys182 and Cys867). In addition, 81 also adducted to Cys627. Auto-ubiquitination assays of Nedd4 mutants featuring alanine substitutions for each of these cysteines suggested that the mode of inhibition of these compounds occurs through blocking the catalytic Cys867. The discovery of these inhibitors could enable the development of therapeutics for various diseases caused by Nedd4 E3 ligase dysregulation.
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Affiliation(s)
- Darren Yong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Stuart R Green
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.
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26
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Tian X, Chen Y, Peng Z, Lin Q, Sun A. NEDD4 E3 ubiquitin ligases: promising biomarkers and therapeutic targets for cancer. Biochem Pharmacol 2023:115641. [PMID: 37307883 DOI: 10.1016/j.bcp.2023.115641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Accumulating evidence has demonstrated that NEDD4 E3 ubiquitin ligase family plays a pivotal oncogenic role in a variety of malignancies via mediating ubiquitin dependent degradation processes. Moreover, aberrant expression of NEDD4 E3 ubiquitin ligases is often indicative of cancer progression and correlated with poor prognosis. In this review, we are going to address association of expression of NEDD4 E3 ubiquitin ligases with cancers, the signaling pathways and the molecular mechanisms by which the NEDD4 E3 ubiquitin ligases regulate oncogenesis and progression, and the therapies targeting the NEDD4 E3 ubiquitin ligases. This review provides the systematic and comprehensive summary of the latest research status of E3 ubiquitin ligases in the NEDD4 subfamily, and proposes that NEDD4 family E3 ubiquitin ligases are promising anti-cancer drug targets, aiming to provide research direction for clinical targeting of NEDD4 E3 ubiquitin ligase therapy.
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Affiliation(s)
- Xianyan Tian
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, China
| | - Yifei Chen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, China
| | - Ziluo Peng
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, China
| | - Qiong Lin
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, China
| | - Aiqin Sun
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, China.
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27
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Souza-Costa LP, Andrade-Chaves JT, Andrade JM, Costa VV, Franco LH. Uncovering new insights into the role of the ubiquitin ligase Smurf1 on the regulation of innate immune signaling and resistance to infection. Front Immunol 2023; 14:1185741. [PMID: 37228615 PMCID: PMC10203584 DOI: 10.3389/fimmu.2023.1185741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 05/27/2023] Open
Abstract
Innate immunity is the body's first line of defense against infections. Innate immune cells express pattern recognition receptors in distinct cellular compartments that are responsible to detect either pathogens-associated molecules or cellular components derived from damaged cells, to trigger intracellular signaling pathways that lead to the activation of inflammatory responses. Inflammation is essential to coordinate immune cell recruitment, pathogen elimination and to keep normal tissue homeostasis. However, uncontrolled, misplaced or aberrant inflammatory responses could lead to tissue damage and drive chronic inflammatory diseases and autoimmunity. In this context, molecular mechanisms that tightly regulate the expression of molecules required for the signaling of innate immune receptors are crucial to prevent pathological immune responses. In this review, we discuss the ubiquitination process and its importance in the regulation of innate immune signaling and inflammation. Then, we summarize the roles of Smurf1, a protein that works on ubiquitination, on the regulation of innate immune signaling and antimicrobial mechanisms, emphasizing its substrates and highlighting its potential as a therapeutic target for infectious and inflammatory conditions.
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Affiliation(s)
- Luiz Pedro Souza-Costa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Josiane Teixeira Andrade-Chaves
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juvana Moreira Andrade
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vivian Vasconcelos Costa
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luis Henrique Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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28
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Zhang R, Shi S. The role of NEDD4 related HECT-type E3 ubiquitin ligases in defective autophagy in cancer cells: molecular mechanisms and therapeutic perspectives. Mol Med 2023; 29:34. [PMID: 36918822 PMCID: PMC10015828 DOI: 10.1186/s10020-023-00628-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/21/2023] [Indexed: 03/15/2023] Open
Abstract
The homologous to the E6-AP carboxyl terminus (HECT)-type E3 ubiquitin ligases are the selective executers in the protein ubiquitination, playing a vital role in modulation of the protein function and stability. Evidence shows the regulatory role of HECT-type E3 ligases in various steps of the autophagic process. Autophagy is an intracellular digestive and recycling process that controls the cellular hemostasis. Defective autophagy is involved in tumorigenesis and has been detected in various types of cancer cells. A growing body of findings indicates that HECT-type E3 ligases, in particular members of the neural precursor cell expressed developmentally downregulated protein 4 (NEDD4) including NEDD4-1, NEDD4-L, SMURFs, WWPs, and ITCH, play critical roles in dysregulation or dysfunction of autophagy in cancer cells. The present review focuses on NEDD4 E3 ligases involved in defective autophagy in cancer cells and discusses their autophagic function in different cancer cells as well as substrates and the signaling pathways in which they participate, conferring a basis for the cancer treatment through the modulating of these E3 ligases.
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Affiliation(s)
- Rui Zhang
- Department of Thoracic Surgery, The Seventh People's Hospital of Chengdu, Chengdu, 610021, Sichuan, People's Republic of China
| | - Shaoqing Shi
- Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China.
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29
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Cutrupi AN, Narayanan RK, Perez-Siles G, Grosz BR, Lai K, Boyling A, Ellis M, Lin RCY, Neumann B, Mao D, Uesugi M, Nicholson GA, Vucic S, Saporta MA, Kennerson ML. Novel gene-intergenic fusion involving ubiquitin E3 ligase UBE3C causes distal hereditary motor neuropathy. Brain 2023; 146:880-897. [PMID: 36380488 PMCID: PMC9976978 DOI: 10.1093/brain/awac424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022] Open
Abstract
Distal hereditary motor neuropathies (dHMNs) are a group of inherited diseases involving the progressive, length-dependent axonal degeneration of the lower motor neurons. There are currently 29 reported causative genes and four disease loci implicated in dHMN. Despite the high genetic heterogeneity, mutations in the known genes account for less than 20% of dHMN cases, with the mutations identified predominantly being point mutations or indels. We have expanded the spectrum of dHMN mutations with the identification of a 1.35 Mb complex structural variation (SV) causing a form of autosomal dominant dHMN (DHMN1 OMIM %182906). Given the complex nature of SV mutations and the importance of studying pathogenic mechanisms in a neuronal setting, we generated a patient-derived DHMN1 motor neuron model harbouring the 1.35 Mb complex insertion. The DHMN1 complex insertion creates a duplicated copy of the first 10 exons of the ubiquitin-protein E3 ligase gene (UBE3C) and forms a novel gene-intergenic fusion sense transcript by incorporating a terminal pseudo-exon from intergenic sequence within the DHMN1 locus. The UBE3C intergenic fusion (UBE3C-IF) transcript does not undergo nonsense-mediated decay and results in a significant reduction of wild-type full-length UBE3C (UBE3C-WT) protein levels in DHMN1 iPSC-derived motor neurons. An engineered transgenic Caenorhabditis elegans model expressing the UBE3C-IF transcript in GABA-ergic motor neurons shows neuronal synaptic transmission deficits. Furthermore, the transgenic animals are susceptible to heat stress, which may implicate defective protein homeostasis underlying DHMN1 pathogenesis. Identification of the novel UBE3C-IF gene-intergenic fusion transcript in motor neurons highlights a potential new disease mechanism underlying axonal and motor neuron degeneration. These complementary models serve as a powerful paradigm for studying the DHMN1 complex SV and an invaluable tool for defining therapeutic targets for DHMN1.
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Affiliation(s)
- Anthony N Cutrupi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ramesh K Narayanan
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Gonzalo Perez-Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Kaitao Lai
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Alexandra Boyling
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ruby C Y Lin
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Brent Neumann
- Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Di Mao
- Institute for Integrated Cell-Material Sciences and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Steve Vucic
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Brain and Nerve Research Centre, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Mario A Saporta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
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30
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Sampson C, Wang Q, Otkur W, Zhao H, Lu Y, Liu X, Piao H. The roles of E3 ubiquitin ligases in cancer progression and targeted therapy. Clin Transl Med 2023; 13:e1204. [PMID: 36881608 PMCID: PMC9991012 DOI: 10.1002/ctm2.1204] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
Ubiquitination is one of the most important post-translational modifications which plays a significant role in conserving the homeostasis of cellular proteins. In the ubiquitination process, ubiquitin is conjugated to target protein substrates for degradation, translocation or activation, dysregulation of which is linked to several diseases including various types of cancers. E3 ubiquitin ligases are regarded as the most influential ubiquitin enzyme owing to their ability to select, bind and recruit target substrates for ubiquitination. In particular, E3 ligases are pivotal in the cancer hallmarks pathways where they serve as tumour promoters or suppressors. The specificity of E3 ligases coupled with their implication in cancer hallmarks engendered the development of compounds that specifically target E3 ligases for cancer therapy. In this review, we highlight the role of E3 ligases in cancer hallmarks such as sustained proliferation via cell cycle progression, immune evasion and tumour promoting inflammation, and in the evasion of apoptosis. In addition, we summarise the application and the role of small compounds that target E3 ligases for cancer treatment along with the significance of targeting E3 ligases as potential cancer therapy.
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Affiliation(s)
- Chibuzo Sampson
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qiuping Wang
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Wuxiyar Otkur
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Haifeng Zhao
- Department of OrthopedicsDalian Second People's HospitalDalianChina
| | - Yun Lu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
- Department of StomatologyDalian Medical UniversityDalianChina
| | - Xiaolong Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Hai‐long Piao
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
- University of Chinese Academy of SciencesBeijingChina
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31
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Connelly EM, Frankel KS, Shaw GS. Parkin and mitochondrial signalling. Cell Signal 2023; 106:110631. [PMID: 36803775 DOI: 10.1016/j.cellsig.2023.110631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Aging, toxic chemicals and changes to the cellular environment are sources of oxidative damage to mitochondria which contribute to neurodegenerative conditions including Parkinson's disease. To counteract this, cells have developed signalling mechanisms to identify and remove select proteins and unhealthy mitochondria to maintain homeostasis. Two important proteins that work in concert to control mitochondrial damage are the protein kinase PINK1 and the E3 ligase parkin. In response to oxidative stress, PINK1 phosphorylates ubiquitin present on proteins at the mitochondrial surface. This signals the translocation of parkin, accelerates further phosphorylation, and stimulates ubiquitination of outer mitochondrial membrane proteins such as Miro1/2 and Mfn1/2. The ubiquitination of these proteins is the key step needed to target them for degradation via the 26S proteasomal machinery or eliminate the entire organelle through mitophagy. This review highlights the signalling mechanisms used by PINK1 and parkin and presents several outstanding questions yet to be resolved.
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Affiliation(s)
- Elizabeth M Connelly
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karling S Frankel
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.
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32
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A Plasmodium falciparum RING Finger E3 Ubiquitin Ligase Modifies the Roles of PfMDR1 and PfCRT in Parasite Drug Responses. Antimicrob Agents Chemother 2023; 67:e0082122. [PMID: 36625569 PMCID: PMC9933707 DOI: 10.1128/aac.00821-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is an important posttranslational regulation mechanism that mediates Plasmodium development and modifies parasite responses to antimalarial drugs. Although mutations in several parasite ubiquitination enzymes have been linked to increased drug tolerance, the molecular mechanisms by which ubiquitination pathways mediate these parasite responses remain largely unknown. Here, we investigate the roles of a Plasmodium falciparum ring finger ubiquitin ligase (PfRFUL) in parasite development and in responses to antimalarial drugs. We engineered a transgenic parasite having the Pfrful gene tagged with an HA-2A-NeoR-glmS sequence to knockdown (KD) Pfrful expression using glucosamine (GlcN). A Western blot analysis of the proteins from GlcN-treated pSLI-HA-NeoR-glmS-tagged (PfRFULg) parasites, relative to their wild-type (Dd2) controls, showed changes in the ubiquitination of numerous proteins. PfRFUL KD rendered the parasites more sensitive to multiple antimalarial drugs, including mefloquine, piperaquine, amodiaquine, and dihydroartemisinin. PfRFUL KD also decreased the protein level of the P. falciparum multiple drug resistance 1 protein (PfMDR1) and altered the ratio of two bands of the P. falciparum chloroquine resistance transporter (PfCRT), suggesting contributions to the changed drug responses by the altered ubiquitination of these two molecules. The inhibition of proteasomal protein degradation by epoxomicin increased the PfRFUL level, suggesting the degradation of PfRFUL by the proteasome pathways, whereas the inhibition of E3 ubiquitin ligase activities by JNJ26854165 reduced the PfRFUL level. This study reveals the potential mechanisms of PfRFUL in modifying the expression of drug transporters and their roles in parasite drug responses. PfRFUL could be a potential target for antimalarial drug development.
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Nyenhuis DA, Rajasekaran R, Watanabe S, Strub MP, Khan M, Powell M, Carter CA, Tjandra N. HECT domain interaction with ubiquitin binding sites on Tsg101-UEV controls HIV-1 egress, maturation, and infectivity. J Biol Chem 2023; 299:102901. [PMID: 36642186 PMCID: PMC9944984 DOI: 10.1016/j.jbc.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The HECT domain of HECT E3 ligases consists of flexibly linked N- and C-terminal lobes, with a ubiquitin (Ub) donor site on the C-lobe that is directly involved in substrate modification. HECT ligases also possess a secondary Ub binding site in the N-lobe, which is thought to play a role in processivity, specificity, or regulation. Here, we report the use of paramagnetic solution NMR to characterize a complex formed between the isolated HECT domain of neural precursor cell-expressed developmentally downregulated 4-1 and the ubiquitin E2 variant (UEV) domain of tumor susceptibility gene 101 (Tsg101). Both proteins are involved in endosomal trafficking, a process driven by Ub signaling, and are hijacked by viral pathogens for particle assembly; however, a direct interaction between them has not been described, and the mechanism by which the HECT E3 ligase contributes to pathogen formation has not been elucidated. We provide evidence for their association, consisting of multiple sites on the neural precursor cell-expressed developmentally downregulated 4-1 HECT domain and elements of the Tsg101 UEV domain involved in noncovalent ubiquitin binding. Furthermore, we show using an established reporter assay that HECT residues perturbed by UEV proximity define determinants of viral maturation and infectivity. These results suggest the UEV interaction is a determinant of HECT activity in Ub signaling. As the endosomal trafficking pathway is hijacked by several human pathogens for egress, the HECT-UEV interaction could represent a potential novel target for therapeutic intervention.
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Affiliation(s)
- David A. Nyenhuis
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rohith Rajasekaran
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan Watanabe
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahfuz Khan
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Michael Powell
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Carol A. Carter
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA,For correspondence: Nico Tjandra; Carol A. Carter
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
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35
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Taibi V, Polo S, Maspero E. Monitoring HECT Ubiquitination Activity In Vitro. Methods Mol Biol 2023; 2602:81-92. [PMID: 36446968 DOI: 10.1007/978-1-0716-2859-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In vitro ubiquitination tools have been employed to mechanistically study the ubiquitin enzymatic cascade. Here, we describe an assay capable to monitor ubiquitin conjugation in real time using the Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) system. The assay requires purified E1 and E2 enzymes, the HECT E3 ligase of choice and two fluorophore-labeled ubiquitins. This single step technique represents an excellent tool to study the enzymatic activity during chain elongation, to compare ligase activity in the presence or absence of the substrate, and to set-up high-throughput screenings for enzymatic activity modulators (i.e., activators or inhibitors).
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Affiliation(s)
- Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy.
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
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Pouyo R, Chung K, Delacroix L, Malgrange B. The ubiquitin-proteasome system in normal hearing and deafness. Hear Res 2022; 426:108366. [PMID: 34645583 DOI: 10.1016/j.heares.2021.108366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022]
Abstract
Post-translational modifications of proteins are essential for the proper development and function of many tissues and organs, including the inner ear. Ubiquitination is a highly selective post-translational modification that involves the covalent conjugation of ubiquitin to a substrate protein. The most common outcome of protein ubiquitination is degradation by the ubiquitin-proteasome system (UPS), preventing the accumulation of misfolded, damaged, and excess proteins. In addition to proteasomal degradation, ubiquitination regulates other cellular processes, such as transcription, translation, endocytosis, receptor activity, and subcellular localization. All of these processes are essential for cochlear development and maintenance, as several studies link impairment of UPS with altered cochlear development and hearing loss. In this review, we provide insight into the well-oiled machinery of UPS with a focus on its confirmed role in normal hearing and deafness and potential therapeutic strategies to prevent and treat UPS-associated hearing loss.
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Affiliation(s)
- Ronald Pouyo
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Keshi Chung
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Laurence Delacroix
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Brigitte Malgrange
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium.
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37
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Pérez-Villegas EM, Ruiz R, Bachiller S, Ventura F, Armengol JA, Rosa JL. The HERC proteins and the nervous system. Semin Cell Dev Biol 2022; 132:5-15. [PMID: 34848147 DOI: 10.1016/j.semcdb.2021.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022]
Abstract
The HERC protein family is one of three subfamilies of Homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases. Six HERC genes have been described in humans, two of which encode Large HERC proteins -HERC1 and HERC2- with molecular weights above 520 kDa that are constitutively expressed in the brain. There is a large body of evidence that mutations in these Large HERC genes produce clinical syndromes in which key neurodevelopmental events are altered, resulting in intellectual disability and other neurological disorders like epileptic seizures, dementia and/or signs of autism. In line with these consequences in humans, two mice carrying mutations in the Large HERC genes have been studied quite intensely: the tambaleante mutant for Herc1 and the Herc2+/530 mutant for Herc2. In both these mutant mice there are clear signs that autophagy is dysregulated, eliciting cerebellar Purkinje cell death and impairing motor control. The tambaleante mouse was the first of these mice to appear and is the best studied, in which the Herc1 mutation elicits: (i) delayed neural transmission in the peripheral nervous system; (ii) impaired learning, memory and motor control; and (iii) altered presynaptic membrane dynamics. In this review, we discuss the information currently available on HERC proteins in the nervous system and their biological activity, the dysregulation of which could explain certain neurodevelopmental syndromes and/or neurodegenerative diseases.
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Affiliation(s)
- Eva M Pérez-Villegas
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville, Spain
| | - Rocío Ruiz
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, Seville, Spain
| | - Sara Bachiller
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Sevilla, Virgen del Rocío University Hospital, CSIC, University of Sevilla, Sevilla, Spain
| | - Francesc Ventura
- Departament de Ciències Fisiològiques, IBIDELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose A Armengol
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville, Spain.
| | - Jose Luis Rosa
- Departament de Ciències Fisiològiques, IBIDELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.
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38
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Sengupta M, Pluciennik A, Merry DE. The role of ubiquitination in spinal and bulbar muscular atrophy. Front Mol Neurosci 2022; 15:1020143. [PMID: 36277484 PMCID: PMC9583669 DOI: 10.3389/fnmol.2022.1020143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a neurodegenerative and neuromuscular genetic disease caused by the expansion of a polyglutamine-encoding CAG tract in the androgen receptor (AR) gene. The AR is an important transcriptional regulator of the nuclear hormone receptor superfamily; its levels are regulated in many ways including by ubiquitin-dependent degradation. Ubiquitination is a post-translational modification (PTM) which plays a key role in both AR transcriptional activity and its degradation. Moreover, the ubiquitin-proteasome system (UPS) is a fundamental component of cellular functioning and has been implicated in diseases of protein misfolding and aggregation, including polyglutamine (polyQ) repeat expansion diseases such as Huntington's disease and SBMA. In this review, we discuss the details of the UPS system, its functions and regulation, and the role of AR ubiquitination and UPS components in SBMA. We also discuss aspects of the UPS that may be manipulated for therapeutic effect in SBMA.
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Affiliation(s)
| | | | - Diane E. Merry
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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39
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Song MS, Pandolfi PP. The HECT family of E3 ubiquitin ligases and PTEN. Semin Cancer Biol 2022; 85:43-51. [PMID: 34129913 PMCID: PMC8665946 DOI: 10.1016/j.semcancer.2021.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/22/2022]
Abstract
Members of the HECT family of E3 ubiquitin ligases have emerged as prominent regulators of PTEN function, subcellular localization and levels. In turn this unfolding regulatory network is allowing for the identification of genes directly involved in both tumorigenesis at large and cancer susceptibility syndromes. While the complexity of this regulatory network is still being unraveled, these new findings are paving the way for novel therapeutic modalities for cancer prevention and therapy as well as for other diseases. Here we will review the signal transduction and therapeutic implications of the cross-talk between HECT family members and PTEN.
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Affiliation(s)
- Min Sup Song
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA.
| | - Pier Paolo Pandolfi
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV89502, USA.
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40
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Abstract
Ubiquitination is a posttranslational modification that regulates a multitude of cellular functions. Pathogens, such as bacteria and viruses, have evolved sophisticated mechanisms that evade or counteract ubiquitin-dependent host responses, or even exploit the ubiquitin system to their own advantage. This is largely done by numerous pathogen virulence factors that encode E3 ligases and deubiquitinases, which are often used as weapons in pathogen-host cell interactions. Moreover, upon pathogen attack, host cellular signaling networks undergo major ubiquitin-dependent changes to protect the host cell, including coordination of innate immunity, remodeling of cellular organelles, reorganization of the cytoskeleton, and reprogramming of metabolic pathways to restrict growth of the pathogen. Here we provide mechanistic insights into ubiquitin regulation of host-pathogen interactions and how it affects bacterial and viral pathogenesis and the organization and response of the host cell.
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Affiliation(s)
- Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany
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41
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Orosa-Puente B, Spoel SH. Harnessing the ubiquitin code to respond to environmental cues. Essays Biochem 2022; 66:111-121. [PMID: 35880291 PMCID: PMC9400065 DOI: 10.1042/ebc20210094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022]
Abstract
Ubiquitination is an essential post-translational signal that allows cells to adapt and respond to environmental stimuli. Substrate modifications range from a single ubiquitin molecule to complex polyubiquitin chains, where diverse chain topologies constitute a code that is utilized to modify the functions of proteins in numerous cellular signalling pathways. Diverse ubiquitin chain topologies are generated by linking the C-terminus of ubiquitin to one of seven lysine residues or the N-terminal methionine 1 residue of the preceding ubiquitin. Cooperative action between a large array of E2 conjugating and E3 ligase enzymes supports the formation of not only homotypic ubiquitin chains but also heterotypic mixed or branched chains. This complex array of chain topologies is recognized by proteins containing linkage-specific ubiquitin-binding domains and regulates numerous cellular pathways. Although many functions of the ubiquitin code in plants remain unknown, recent work suggests that specific chain topologies are associated with particular molecular processes. Deciphering the ubiquitin code and how plants utilize it to cope with the changing environment is essential to understand the regulatory mechanisms that underpin myriad stress responses and establishment of environmental tolerance.
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Affiliation(s)
- Beatriz Orosa-Puente
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 5JF, U.K
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 5JF, U.K
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42
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Agostino M, McKenzie F, Buck C, Woodward KJ, Atkinson VJ, Azmanov DN, Heng JIT. Studying Disease-Associated UBE3A Missense Variants Using Enhanced Sampling Molecular Simulations. ACS OMEGA 2022; 7:25039-25045. [PMID: 35910155 PMCID: PMC9330222 DOI: 10.1021/acsomega.2c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Missense variants in UBE3A underlie neurodevelopmental conditions such as Angelman Syndrome and Autism Spectrum Disorder, but the underlying molecular pathological consequences on protein folding and function are poorly understood. Here, we report a novel, maternally inherited, likely pathogenic missense variant in UBE3A (NM_000462.4(UBE3A_v001):(c.1841T>C) (p.(Leu614Pro))) in a child that presented with myoclonic epilepsy from 14 months, subsequent developmental regression from 16 months, and additional features consistent with Angelman Syndrome. To understand the impact of p.(Leu614Pro) on UBE3A, we used adiabatic biased molecular dynamics and metadynamics simulations to investigate conformational differences from wildtype proteins. Our results suggest that Leu614Pro substitution leads to less efficient binding and substrate processing compared to wildtype. Our results support the use of enhanced sampling molecular simulations to investigate the impact of missense UBE3A variants on protein function that underlies neurodevelopment and human disorders.
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Affiliation(s)
- Mark Agostino
- Curtin
Health Innovation Research Institute, Curtin
University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
- Curtin
Institute for Computation, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Fiona McKenzie
- Genetic
Services of Western Australia, King Edward
Memorial Hospital, 374
Bagot Road, Subiaco, Perth, Western Australia 6008, Australia
- School
of Paediatrics and Child Health, University
of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia 6009, Australia
| | - Chloe Buck
- School
of Allergy and Clinical Immunology, University
of Cape Town, Cape Town 7925, South Africa
| | - Karen J. Woodward
- Diagnostic
Genomics, PathWest Laboratory Medicine, QEII Medical Centre E Block, Perth, Western Australia 6009, Australia
- School
of Biomedical Sciences, University of Western
Australia, 35 Stirling
Highway, Crawley, Perth, Western Australia 6009, Australia
| | - Vanessa J. Atkinson
- Diagnostic
Genomics, PathWest Laboratory Medicine, QEII Medical Centre E Block, Perth, Western Australia 6009, Australia
| | - Dimitar N. Azmanov
- Diagnostic
Genomics, PathWest Laboratory Medicine, QEII Medical Centre E Block, Perth, Western Australia 6009, Australia
| | - Julian Ik-Tsen Heng
- Curtin
Health Innovation Research Institute, Curtin
University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
- Curtin
Medical School, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
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43
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Zhao Y, Li J, Chen J, Ye M, Jin X. Functional roles of E3 ubiquitin ligases in prostate cancer. J Mol Med (Berl) 2022; 100:1125-1144. [PMID: 35816219 DOI: 10.1007/s00109-022-02229-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/16/2022]
Abstract
Prostate cancer (PCa) is a malignant epithelial tumor of the prostate gland with a high male cancer incidence. Numerous studies indicate that abnormal function of ubiquitin-proteasome system (UPS) is associated with the progression and metastasis of PCa. E3 ubiquitin ligases, key components of UPS, determine the specificity of substrates, and substantial advances of E3 ubiquitin ligases have been reached recently. Herein, we introduce the structures and functions of E3 ubiquitin ligases and summarize the mechanisms of E3 ubiquitin ligases-related PCa signaling pathways. In addition, some progresses in the development of inhibitors targeting E3 ubiquitin ligases are also included.
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Affiliation(s)
- Yiting Zhao
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.,Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Jinyun Li
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Jun Chen
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Meng Ye
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiaofeng Jin
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
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44
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Jiang H, Chiang CY, Chen Z, Nathan S, D'Agostino G, Paulo JA, Song G, Zhu H, Gabelli SB, Cole PA. Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates. J Biol Chem 2022; 298:101854. [PMID: 35331737 PMCID: PMC9034101 DOI: 10.1016/j.jbc.2022.101854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022] Open
Abstract
WWP2 is a HECT E3 ligase that targets protein Lys residues for ubiquitination and is comprised of an N-terminal C2 domain, four central WW domains, and a C-terminal catalytic HECT domain. The peptide segment between the middle WW domains, the 2,3-linker, is known to autoinhibit the catalytic domain, and this autoinhibition can be relieved by phosphorylation at Tyr369. Several protein substrates of WWP2 have been identified, including the tumor suppressor lipid phosphatase PTEN, but the full substrate landscape and biological functions of WWP2 remain to be elucidated. Here, we used protein microarray technology and the activated enzyme phosphomimetic mutant WWP2Y369E to identify potential WWP2 substrates. We identified 31 substrate hits for WWP2Y369E using protein microarrays, of which three were known autophagy receptors (NDP52, OPTN, and SQSTM1). These three hits were validated with in vitro and cell-based transfection assays and the Lys ubiquitination sites on these proteins were mapped by mass spectrometry. Among the mapped ubiquitin sites on these autophagy receptors, many had been previously identified in the endogenous proteins. Finally, we observed that WWP2 KO SH-SH5Y neuroblastoma cells using CRISPR-Cas9 showed a defect in mitophagy, which could be rescued by WWP2Y369E transfection. These studies suggest that WWP2-mediated ubiquitination of the autophagy receptors NDP52, OPTN, and SQSTM1 may positively contribute to the regulation of autophagy.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Claire Y Chiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zan Chen
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sara Nathan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Gabriel D'Agostino
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
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45
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Endocytosis at the Crossroad of Polarity and Signaling Regulation: Learning from Drosophila melanogaster and Beyond. Int J Mol Sci 2022; 23:ijms23094684. [PMID: 35563080 PMCID: PMC9101507 DOI: 10.3390/ijms23094684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
Cellular trafficking through the endosomal–lysosomal system is essential for the transport of cargo proteins, receptors and lipids from the plasma membrane inside the cells and across membranous organelles. By acting as sorting stations, vesicle compartments direct the fate of their content for degradation, recycling to the membrane or transport to the trans-Golgi network. To effectively communicate with their neighbors, cells need to regulate their compartmentation and guide their signaling machineries to cortical membranes underlying these contact sites. Endosomal trafficking is indispensable for the polarized distribution of fate determinants, adaptors and junctional proteins. Conversely, endocytic machineries cooperate with polarity and scaffolding components to internalize receptors and target them to discrete membrane domains. Depending on the cell and tissue context, receptor endocytosis can terminate signaling responses but can also activate them within endosomes that act as signaling platforms. Therefore, cell homeostasis and responses to environmental cues rely on the dynamic cooperation of endosomal–lysosomal machineries with polarity and signaling cues. This review aims to address advances and emerging concepts on the cooperative regulation of endocytosis, polarity and signaling, primarily in Drosophila melanogaster and discuss some of the open questions across the different cell and tissue types that have not yet been fully explored.
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Lohraseb I, McCarthy P, Secker G, Marchant C, Wu J, Ali N, Kumar S, Daly RJ, Harvey NL, Kawabe H, Kleifeld O, Wiszniak S, Schwarz Q. Global ubiquitinome profiling identifies NEDD4 as a regulator of Profilin 1 and actin remodelling in neural crest cells. Nat Commun 2022; 13:2018. [PMID: 35440627 PMCID: PMC9018756 DOI: 10.1038/s41467-022-29660-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 03/24/2022] [Indexed: 01/02/2023] Open
Abstract
The ubiquitin ligase NEDD4 promotes neural crest cell (NCC) survival and stem-cell like properties to regulate craniofacial and peripheral nervous system development. However, how ubiquitination and NEDD4 control NCC development remains unknown. Here we combine quantitative analysis of the proteome, transcriptome and ubiquitinome to identify key developmental signalling pathways that are regulated by NEDD4. We report 276 NEDD4 targets in NCCs and show that loss of NEDD4 leads to a pronounced global reduction in specific ubiquitin lysine linkages. We further show that NEDD4 contributes to the regulation of the NCC actin cytoskeleton by controlling ubiquitination and turnover of Profilin 1 to modulate filamentous actin polymerization. Taken together, our data provide insights into how NEDD4-mediated ubiquitination coordinates key regulatory processes during NCC development. Here the authors combine multi-omics approaches to uncover a role for ubiquitination and the ubiquitin ligase NEDD4 in targeting the actin binding protein Profilin 1 to regulate actin polymerisation in neural crest cells.
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Affiliation(s)
- Iman Lohraseb
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Peter McCarthy
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Genevieve Secker
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Ceilidh Marchant
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Jianmin Wu
- Kinghorn Cancer Centre & Cancer Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Naveid Ali
- Bone Therapeutics Group, Bone Biology Division, Garvan Institute of Medical Research, Sydney, 2010, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Roger J Daly
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, 3800, Australia
| | - Natasha L Harvey
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, Goettingen, 37075, Germany.,Department of Pharmacology, Gunma University Graduate School of Medicine, Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Sophie Wiszniak
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, GPO Box 2471, Adelaide, 5000, Australia.
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Haouari S, Vourc’h P, Jeanne M, Marouillat S, Veyrat-Durebex C, Lanznaster D, Laumonnier F, Corcia P, Blasco H, Andres CR. The Roles of NEDD4 Subfamily of HECT E3 Ubiquitin Ligases in Neurodevelopment and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23073882. [PMID: 35409239 PMCID: PMC8999422 DOI: 10.3390/ijms23073882] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin pathway regulates the function of many proteins and controls cellular protein homeostasis. In recent years, it has attracted great interest in neurodevelopmental and neurodegenerative diseases. Here, we have presented the first review on the roles of the 9 proteins of the HECT E3 ligase NEDD4 subfamily in the development and function of neurons in the central nervous system (CNS). We discussed their regulation and their direct or indirect involvement in neurodevelopmental diseases, such as intellectual disability, and neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease or Amyotrophic Lateral Sclerosis. Further studies on the roles of these proteins, their regulation and their targets in neurons will certainly contribute to a better understanding of neuronal function and dysfunction, and will also provide interesting information for the development of therapeutics targeting them.
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Affiliation(s)
- Shanez Haouari
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
| | - Patrick Vourc’h
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Biochimie et Biologie Moléculaire, 37044 Tours, France
- Correspondence: ; Tel.: +33-(0)2-34-37-89-10; Fax: +33-(0)2-47-36-61-85
| | - Médéric Jeanne
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Génétique, 37044 Tours, France
| | - Sylviane Marouillat
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
| | - Charlotte Veyrat-Durebex
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Biochimie et Biologie Moléculaire, 37044 Tours, France
| | - Débora Lanznaster
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
| | - Frédéric Laumonnier
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
| | - Philippe Corcia
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Neurologie, 37044 Tours, France
| | - Hélène Blasco
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Biochimie et Biologie Moléculaire, 37044 Tours, France
| | - Christian R. Andres
- UMR 1253, iBrain, Université de Tours, Inserm, 37044 Tours, France; (S.H.); (M.J.); (S.M.); (C.V.-D.); (D.L.); (F.L.); (P.C.); (H.B.); (C.R.A.)
- CHRU de Tours, Service de Biochimie et Biologie Moléculaire, 37044 Tours, France
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Modulating the Ubiquitin–Proteasome System: A Therapeutic Strategy for Autoimmune Diseases. Cells 2022; 11:cells11071093. [PMID: 35406655 PMCID: PMC8997991 DOI: 10.3390/cells11071093] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune, neurodegenerative disease associated with the central nervous system (CNS). Autoimmunity is caused by an abnormal immune response to self-antigens, which results in chronic inflammation and tissue death. Ubiquitination is a post-translational modification in which ubiquitin molecules are attached to proteins by ubiquitinating enzymes, and then the modified proteins are degraded by the proteasome system. In addition to regulating proteasomal degradation of proteins, ubiquitination also regulates other cellular functions that are independent of proteasomal degradation. It plays a vital role in intracellular protein turnover and immune signaling and responses. The ubiquitin–proteasome system (UPS) is primarily responsible for the nonlysosomal proteolysis of intracellular proteins. The 26S proteasome is a multicatalytic adenosine-triphosphate-dependent protease that recognizes ubiquitin covalently attached to particular proteins and targets them for degradation. Damaged, oxidized, or misfolded proteins, as well as regulatory proteins that govern many essential cellular functions, are removed by this degradation pathway. When this system is affected, cellular homeostasis is altered, resulting in the induction of a range of diseases. This review discusses the biochemistry and molecular biology of the UPS, including its role in the development of MS and proteinopathies. Potential therapies and targets involving the UPS are also addressed.
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Lacoursiere RE, Hadi D, Shaw GS. Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road. Biomolecules 2022; 12:biom12030467. [PMID: 35327659 PMCID: PMC8946176 DOI: 10.3390/biom12030467] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is controlled by a series of E1, E2, and E3 enzymes that can ligate ubiquitin to cellular proteins and dictate the turnover of a substrate and the outcome of signalling events such as DNA damage repair and cell cycle. This process is complex due to the combinatorial power of ~35 E2 and ~1000 E3 enzymes involved and the multiple lysine residues on ubiquitin that can be used to assemble polyubiquitin chains. Recently, mass spectrometric methods have identified that most enzymes in the ubiquitination cascade can be further modified through acetylation or phosphorylation under particular cellular conditions and altered modifications have been noted in different cancers and neurodegenerative diseases. This review provides a cohesive summary of ubiquitination, acetylation, and phosphorylation sites in ubiquitin, the human E1 enzyme UBA1, all E2 enzymes, and some representative E3 enzymes. The potential impacts these post-translational modifications might have on each protein function are highlighted, as well as the observations from human disease.
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50
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Yu Z, Li H, Zhu J, Wang H, Jin X. The roles of E3 ligases in Hepatocellular carcinoma. Am J Cancer Res 2022; 12:1179-1214. [PMID: 35411231 PMCID: PMC8984888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023] Open
Abstract
Hepatocarcinogenesis is a complex multistep biological process involving genetic and epigenetic alterations that are accompanied by activation of oncoproteins and inactivation of tumor suppressors, which in turn results in Hepatocellular carcinoma (HCC), one of the common tumors with high morbidity and mortality worldwide. The ubiquitin-proteasome system (UPS) is the key to protein degradation and regulation of physiological and pathological processes, and E3 ligases are key enzymes in the UPS that contain a variety of subfamily proteins involved in the regulation of some common signal pathways in HCC. There is growing evidence that many structural or functional dysfunctions of E3 are engaged in the development and progression of HCC. Herein, we review recent research advances in HCC-associated E3 ligases, describe their structure, classification, functional roles, and discuss some mechanisms of the abnormal activation or inactivation of the HCC-associated signal pathway due to the binding of E3 to known substrates. In addition, given the success of proteasome inhibitors in the treatment of malignant cancers, we characterize the current knowledge and future prospects for targeted therapies against aberrant E3 in HCC.
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Affiliation(s)
- Zongdong Yu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Hong Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Jie Zhu
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Haibiao Wang
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of Lihuili Hospital, Ningbo UniversityNingbo 315040, Zhejiang, China
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