1
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Zheng LL, Wang LT, Pang YW, Sun LP, Shi L. Recent advances in the development of deubiquitinases inhibitors as antitumor agents. Eur J Med Chem 2024; 266:116161. [PMID: 38262120 DOI: 10.1016/j.ejmech.2024.116161] [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: 11/01/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Ubiquitination is a type of post-translational modification that covalently links ubiquitin to a target protein, which plays a critical role in modulating protein activity, stability, and localization. In contrast, this process is reversed by deubiquitinases (DUBs), which remove ubiquitin from ubiquitinated substrates. Dysregulation of DUBs is associated with several human diseases, such as cancer, inflammation, neurodegenerative disorders, and autoimmune diseases. Thus, DUBs have become promising targets for drug development. Although the physiological and pathological effects of DUBs are increasingly well understood, the clinical drug discovery of selective DUB inhibitors has been challenging. Herein, we summarize the structures and functions of main classes of DUBs and discuss the recent progress in developing selective small-molecule DUB inhibitors as antitumor agents.
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Affiliation(s)
- Li-Li Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ting Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ye-Wei Pang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ping Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lei Shi
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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2
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Buneeva O, Medvedev A. Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson's Disease. Int J Mol Sci 2024; 25:1303. [PMID: 38279302 PMCID: PMC10816476 DOI: 10.3390/ijms25021303] [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: 12/25/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson's disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein-protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein-protein interactions, which still need better characterization.
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Affiliation(s)
| | - Alexei Medvedev
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia;
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3
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Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP. Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. ACS Chem Biol 2023; 18:2003-2013. [PMID: 37642399 PMCID: PMC10510154 DOI: 10.1021/acschembio.3c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.
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Affiliation(s)
- Jin Gan
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jelle de Vries
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Rayman T. N. Tjokrodirijo
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Robbert Q. Kim
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Vito Pol
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Jacques Neefjes
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Hans van Dam
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Paul P. Geurink
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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4
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Park J, Shin SC, Jin KS, Lim MJ, Kim Y, Kim EE, Song EJ. USP35 dimer prevents its degradation by E3 ligase CHIP through auto-deubiquitinating activity. Cell Mol Life Sci 2023; 80:112. [PMID: 37004621 PMCID: PMC11073304 DOI: 10.1007/s00018-023-04740-9] [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: 11/14/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 04/04/2023]
Abstract
Recently, a number of reports on the importance of USP35 in cancer have been published. However, very little is known about the exact mechanism by which USP35 activity is regulated. Here, we show the possible regulation of USP35 activity and the structural specificity affecting its function by analyzing various fragments of USP35. Interestingly, the catalytic domain of USP35 alone does not exhibit deubiquitinating activity; in contrast, the C-terminal domain and insertion region in the catalytic domain is required for full USP35 activity. Additionally, through its C-terminal domain, USP35 forms a homodimer that prevents USP35 degradation. CHIP bound to HSP90 interacts with and ubiquitinates USP35. However, when fully functional USP35 undergoes auto-deubiquitination, which attenuates CHIP-mediated ubiquitination. Finally, USP35 dimer is required for deubiquitination of the substrate Aurora B and regulation of faithful mitotic progression. The properties of USP35 identified in this study are a unique homodimer structure, regulation of deubiquitinating activity through this, and utilization of a novel E3 ligase involved in USP35 auto-deubiquitination, which adds another complexity to the regulation of deubiquitinating enzymes.
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Affiliation(s)
- Jinyoung Park
- Biomedical Research Division, Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio‑Medical Science and Technology, KIST‑School, University of Science and Technology (UST), Seoul, 02792, Korea
| | - Sang Chul Shin
- Research Resources Division, Technological Convergence Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 37673, Kyungbuk, Korea
| | - Min Joon Lim
- Biomedical Research Division, Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Yeojin Kim
- Biomedical Research Division, Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Division, Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea.
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Korea.
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5
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The Mechano-Ubiquitinome of Articular Cartilage: Differential Ubiquitination and Activation of a Group of ER-Associated DUBs and ER Stress Regulators. Mol Cell Proteomics 2022; 21:100419. [PMID: 36182100 PMCID: PMC9708921 DOI: 10.1016/j.mcpro.2022.100419] [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: 03/15/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 01/18/2023] Open
Abstract
Understanding how connective tissue cells respond to mechanical stimulation is important to human health and disease processes in musculoskeletal diseases. Injury to articular cartilage is a key risk factor in predisposition to tissue damage and degenerative osteoarthritis. Recently, we have discovered that mechanical injury to connective tissues including murine and porcine articular cartilage causes a significant increase in lysine-63 polyubiquitination. Here, we identified the ubiquitin signature that is unique to injured articular cartilage tissue upon mechanical injury (the "mechano-ubiquitinome"). A total of 463 ubiquitinated peptides were identified, with an enrichment of ubiquitinated peptides of proteins involved in protein processing in the endoplasmic reticulum (ER), also known as the ER-associated degradation response, including YOD1, BRCC3, ATXN3, and USP5 as well as the ER stress regulators, RAD23B, VCP/p97, and Ubiquilin 1. Enrichment of these proteins suggested an injury-induced ER stress response and, for instance, ER stress markers DDIT3/CHOP and BIP/GRP78 were upregulated following cartilage injury on the protein and gene expression levels. Similar ER stress induction was also observed in response to tail fin injury in zebrafish larvae, suggesting a generic response to tissue injury. Furthermore, a rapid increase in global DUB activity following injury and significant activity in human osteoarthritic cartilage was observed using DUB-specific activity probes. Combined, these results implicate the involvement of ubiquitination events and activation of a set of DUBs and ER stress regulators in cellular responses to cartilage tissue injury and in osteoarthritic cartilage tissues. This link through the ER-associated degradation pathway makes this protein set attractive for further investigation in in vivo models of tissue injury and for targeting in osteoarthritis and related musculoskeletal diseases.
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6
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Grethe C, Schmidt M, Kipka GM, O'Dea R, Gallant K, Janning P, Gersch M. Structural basis for specific inhibition of the deubiquitinase UCHL1. Nat Commun 2022; 13:5950. [PMID: 36216817 PMCID: PMC9549030 DOI: 10.1038/s41467-022-33559-4] [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: 04/29/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022] Open
Abstract
Ubiquitination regulates protein homeostasis and is tightly controlled by deubiquitinases (DUBs). Loss of the DUB UCHL1 leads to neurodegeneration, and its dysregulation promotes cancer metastasis and invasiveness. Small molecule probes for UCHL1 and DUBs in general could help investigate their function, yet specific inhibitors and structural information are rare. Here we report the potent and non-toxic chemogenomic pair of activity-based probes GK13S and GK16S for UCHL1. Biochemical characterization of GK13S demonstrates its stereoselective inhibition of cellular UCHL1. The crystal structure of UCHL1 in complex with GK13S shows the enzyme locked in a hybrid conformation of apo and Ubiquitin-bound states, which underlies its UCHL1-specificity within the UCH DUB family. Phenocopying a reported inactivating mutation of UCHL1 in mice, GK13S, but not GK16S, leads to reduced levels of monoubiquitin in a human glioblastoma cell line. Collectively, we introduce a set of structurally characterized, chemogenomic probes suitable for the cellular investigation of UCHL1. The deubiquitinase UCHL1 has been linked to cancer invasiveness and neurodegeneration yet its molecular roles have remained poorly defined. Here the authors reveal the structural basis for how UCHL1 can be specifically inhibited and how chemogenomic probes can be used to dissect its functions in living cells.
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Affiliation(s)
- Christian Grethe
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Mirko Schmidt
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Gian-Marvin Kipka
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Rachel O'Dea
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Kai Gallant
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Str. 11, Dortmund, Germany
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany. .,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany.
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7
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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8
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Atypical Ubiquitination and Parkinson's Disease. Int J Mol Sci 2022; 23:ijms23073705. [PMID: 35409068 PMCID: PMC8998352 DOI: 10.3390/ijms23073705] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Ubiquitination (the covalent attachment of ubiquitin molecules to target proteins) is one of the main post-translational modifications of proteins. Historically, the type of polyubiquitination, which involves K48 lysine residues of the monomeric ubiquitin, was the first studied type of ubiquitination. It usually targets proteins for their subsequent proteasomal degradation. All the other types of ubiquitination, including monoubiquitination; multi-monoubiquitination; and polyubiquitination involving lysine residues K6, K11, K27, K29, K33, and K63 and N-terminal methionine, were defined as atypical ubiquitination (AU). Good evidence now exists that AUs, participating in the regulation of various cellular processes, are crucial for the development of Parkinson's disease (PD). These AUs target various proteins involved in PD pathogenesis. The K6-, K27-, K29-, and K33-linked polyubiquitination of alpha-synuclein, the main component of Lewy bodies, and DJ-1 (another PD-associated protein) is involved in the formation of insoluble aggregates. Multifunctional protein kinase LRRK2 essential for PD is subjected to K63- and K27-linked ubiquitination. Mitophagy mediated by the ubiquitin ligase parkin is accompanied by K63-linked autoubiquitination of parkin itself and monoubiquitination and polyubiquitination of mitochondrial proteins with the formation of both classical K48-linked ubiquitin chains and atypical K6-, K11-, K27-, and K63-linked polyubiquitin chains. The ubiquitin-specific proteases USP30, USP33, USP8, and USP15, removing predominantly K6-, K11-, and K63-linked ubiquitin conjugates, antagonize parkin-mediated mitophagy.
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9
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Magits W, Sablina AA. The regulation of the protein interaction network by monoubiquitination. Curr Opin Struct Biol 2022; 73:102333. [PMID: 35176591 DOI: 10.1016/j.sbi.2022.102333] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/24/2021] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
The conjugation of a single ubiquitin or monoubiquitination acts as a versatile signal that can have both degradative and non-degradative functions. The latter is of particular interest as emerging evidence indicates that ubiquitin-driven alterations of the protein interaction landscape play a key role in multiple signaling pathways. Whereas early studies were focused on how monoubiquitination alters the interactions of proteins containing ubiquitin-binding domains, more recent reports demonstrate that ubiquitin conjugation can also affect the binding mode by changing the surface of the ubiquitinated substrate. Furthermore, monoubiquitination modulates the interactions with other macromolecules, such as DNA or lipids, underscoring the diverse role of monoubiquitination in cellular processes. In this review, we discussed how monoubiquitination achieves its function by modulating the interaction landscape.
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Affiliation(s)
- Wout Magits
- VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Anna A Sablina
- VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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10
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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11
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Davies CW, Vidal SE, Phu L, Sudhamsu J, Hinkle TB, Chan Rosenberg S, Schumacher FR, Zeng YJ, Schwerdtfeger C, Peterson AS, Lill JR, Rose CM, Shaw AS, Wertz IE, Kirkpatrick DS, Koerber JT. Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W. Nat Commun 2021; 12:4608. [PMID: 34326324 PMCID: PMC8322077 DOI: 10.1038/s41467-021-24669-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solve the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. We use these antibodies in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates include UCHL1 and UCHL5, where N-terminal ubiquitination distinctly alters deubiquitinase (DUB) activity. This work describes an antibody toolkit for enrichment and global profiling of endogenous N-terminal ubiquitination sites, while revealing functionally relevant substrates of UBE2W.
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Affiliation(s)
- Christopher W. Davies
- grid.418158.10000 0004 0534 4718Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA USA
| | - Simon E. Vidal
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA
| | - Lilian Phu
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Jawahar Sudhamsu
- grid.418158.10000 0004 0534 4718Department of Structural Biology, Genentech, Inc., South San Francisco, CA USA
| | - Trent B. Hinkle
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Scott Chan Rosenberg
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA
| | - Frances-Rose Schumacher
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Yi Jimmy Zeng
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | | | - Andrew S. Peterson
- grid.418158.10000 0004 0534 4718Department of Molecular Biology, Genentech, Inc., South San Francisco, CA USA
| | - Jennie R. Lill
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Christopher M. Rose
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Andrey S. Shaw
- grid.418158.10000 0004 0534 4718Research Biology, Genentech, Inc., South San Francisco, CA USA
| | - Ingrid E. Wertz
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA ,grid.419971.3Present Address: Bristol Myers Squibb, 1000 Sierra Point Parkway, Brisbane, CA USA
| | - Donald S. Kirkpatrick
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA ,Present Address: Interline Therapeutics, South San Francisco, CA USA
| | - James T. Koerber
- grid.418158.10000 0004 0534 4718Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA USA
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12
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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13
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Hou Z, Shi W, Feng J, Wang W, Zheng E, Lin H, Yu C, Li L. Self-stabilizing regulation of deubiquitinating enzymes in an enzymatic activity-dependent manner. Int J Biol Macromol 2021; 181:1081-1091. [PMID: 33864866 DOI: 10.1016/j.ijbiomac.2021.04.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Abstract
Deubiquitinating enzymes (DUBs) play important roles in many physiological and pathological processes by modulating the ubiquitination of their substrates. DUBs undergo post-translational modifications including ubiquitination. However, whether DUBs can reverse their own ubiquitination and regulate their own protein stability requires further investigation. To answer this question, we screened an expression library of DUBs and their enzymatic activity mutants and found that some DUBs regulated their own protein stability in an enzymatic activity- and homomeric interaction-dependent manner. Taking Ubiquitin-specific-processing protease 29 (USP29) as an example, we found that USP29 deubiquitinates itself and protects itself from proteasomal degradation. We also revealed that the N-terminal region of USP29 is critical for its protein stability. Taken together, our work demonstrates that at least some DUBs regulate their own ubiquitination and protein stability. Our findings provide novel molecular insight into the diverse regulation of DUBs.
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Affiliation(s)
- Zhenzhu Hou
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wanyan Shi
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jinan Feng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei Wang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Enrun Zheng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Hanbin Lin
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Cheng Yu
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lisheng Li
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou, China.
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14
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Regulation of Deubiquitinating Enzymes by Post-Translational Modifications. Int J Mol Sci 2020; 21:ijms21114028. [PMID: 32512887 PMCID: PMC7312083 DOI: 10.3390/ijms21114028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins.
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15
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Damianou A, Burge RJ, Catta-Preta CMC, Geoghegan V, Nievas YR, Newling K, Brown E, Burchmore R, Rodenko B, Mottram JC. Essential roles for deubiquitination in Leishmania life cycle progression. PLoS Pathog 2020; 16:e1008455. [PMID: 32544189 PMCID: PMC7319358 DOI: 10.1371/journal.ppat.1008455] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/26/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
The parasitic protozoan Leishmania requires proteasomal, autophagic and lysosomal proteolytic pathways to enact the extensive cellular remodelling that occurs during its life cycle. The proteasome is essential for parasite proliferation, yet little is known about the requirement for ubiquitination/deubiquitination processes in growth and differentiation. Activity-based protein profiling of L. mexicana C12, C19 and C65 deubiquitinating cysteine peptidases (DUBs) revealed DUB activity remains relatively constant during differentiation of procyclic promastigote to amastigote. However, when life cycle phenotyping (bar-seq) was performed on a pool including 15 barcoded DUB null mutants created in promastigotes using CRISPR-Cas9, significant loss of fitness was observed during differentiation and intracellular infection. DUBs 4, 7, and 13 are required for successful transformation from metacyclic promastigote to amastigote and DUBs 3, 5, 6, 8, 10, 11 and 14 are required for normal amastigote proliferation in mice. DUBs 1, 2, 12 and 16 are essential for promastigote viability and the essential role of DUB2 in establishing infection was demonstrated using DiCre inducible gene deletion in vitro and in vivo. DUB2 is found in the nucleus and interacts with nuclear proteins associated with transcription/chromatin dynamics, mRNA splicing and mRNA capping. DUB2 has broad linkage specificity, cleaving all the di-ubiquitin chains except for Lys27 and Met1. Our study demonstrates the crucial role that DUBs play in differentiation and intracellular survival of Leishmania and that amastigotes are exquisitely sensitive to disruption of ubiquitination homeostasis.
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Affiliation(s)
- Andreas Damianou
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rebecca J. Burge
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | | | - Vincent Geoghegan
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Y. Romina Nievas
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Katherine Newling
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Elaine Brown
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Richard Burchmore
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Boris Rodenko
- UbiQ Bio BV, Amsterdam Science Park, The Netherlands
| | - Jeremy C. Mottram
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
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16
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Hussain S, Bedekovics T, Ali A, Zaid O, May DG, Roux KJ, Galardy PJ. A cysteine near the C-terminus of UCH-L1 is dispensable for catalytic activity but is required to promote AKT phosphorylation, eIF4F assembly, and malignant B-cell survival. Cell Death Discov 2019; 5:152. [PMID: 31839994 PMCID: PMC6904616 DOI: 10.1038/s41420-019-0231-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/24/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
The enzyme UCH-L1 is a neuro-endocrine and germinal center B-cell marker that contributes to the development and aggressive behavior of mature B-cell malignancies. While mutations in this enzyme have been associated with Parkinson's disease, relatively little is known about the molecular features associated with the biochemical activities of UCH-L1. Here we use a survival-based complementation assay and site-directed mutagenesis and identify a novel role for the C-terminus of UCH-L1 in supporting cell survival. The C220 residue is required for UCH-L1 to promote the assembly of mTOR complex 2 and phosphorylation of the pro-survival kinase AKT. While this residue was previously described as a potential farnesylation site, destruction of the putative CAAX motif by adding a C-terminal epitope tag did not interfere with cell survival, indicating an alternate mechanism. We used proximity-based proteomics comparing the proteomes of wild-type and C220S UCH-L1 and identified a selective loss of association with RNA-binding proteins including components of the translation initiation machinery. As a consequence, the C220S mutant did not promote the assembly of the eIF4F complex. These data identify a novel role for the C-terminus of UCH-L1 in supporting pro-survival and metabolic activities in malignant B-cells. This finding may lead to the development of therapeutics with selective activity towards malignancy that potentially avoid neuronal toxicities.
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Affiliation(s)
- Sajjad Hussain
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Tibor Bedekovics
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Asma Ali
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Omar Zaid
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Danielle G. May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104 USA
| | - Kyle J. Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104 USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105 USA
| | - Paul J. Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905 USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Pediatric Hematology-Oncology, Mayo Clinic, Rochester, MN 55905 USA
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17
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Functional analysis of deubiquitylating enzymes in tumorigenesis and development. Biochim Biophys Acta Rev Cancer 2019; 1872:188312. [DOI: 10.1016/j.bbcan.2019.188312] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
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18
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Karimi-Moghadam A, Charsouei S, Bell B, Jabalameli MR. Parkinson Disease from Mendelian Forms to Genetic Susceptibility: New Molecular Insights into the Neurodegeneration Process. Cell Mol Neurobiol 2018; 38:1153-1178. [PMID: 29700661 PMCID: PMC6061130 DOI: 10.1007/s10571-018-0587-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022]
Abstract
Parkinson disease (PD) is known as a common progressive neurodegenerative disease which is clinically diagnosed by the manifestation of numerous motor and nonmotor symptoms. PD is a genetically heterogeneous disorder with both familial and sporadic forms. To date, researches in the field of Parkinsonism have identified 23 genes or loci linked to rare monogenic familial forms of PD with Mendelian inheritance. Biochemical studies revealed that the products of these genes usually play key roles in the proper protein and mitochondrial quality control processes, as well as synaptic transmission and vesicular recycling pathways within neurons. Despite this, large number of patients affected with PD typically tends to show sporadic forms of disease with lack of a clear family history. Recent genome-wide association studies (GWAS) meta-analyses on the large sporadic PD case-control samples from European populations have identified over 12 genetic risk factors. However, the genetic etiology that underlies pathogenesis of PD is also discussed, since it remains unidentified in 40% of all PD-affected cases. Nowadays, with the emergence of new genetic techniques, international PD genomics consortiums and public online resources such as PDGene, there are many hopes that future large-scale genetics projects provide further insights into the genetic etiology of PD and improve diagnostic accuracy and therapeutic clinical trial designs.
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Affiliation(s)
- Amin Karimi-Moghadam
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran
| | - Saeid Charsouei
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Benjamin Bell
- Human Genetics & Genomic Medicine, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Mohammad Reza Jabalameli
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran.
- Human Genetics & Genomic Medicine, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK.
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19
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Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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20
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Piao S, Pei HZ, Huang B, Baek SH. Ovarian tumor domain-containing protein 1 deubiquitinates and stabilizes p53. Cell Signal 2017; 33:22-29. [DOI: 10.1016/j.cellsig.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/22/2022]
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21
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Liu H, Li W, Rose ME, Hickey RW, Chen J, Uechi GT, Balasubramani M, Day BW, Patel KV, Graham SH. The point mutation UCH-L1 C152A protects primary neurons against cyclopentenone prostaglandin-induced cytotoxicity: implications for post-ischemic neuronal injury. Cell Death Dis 2015; 6:e1966. [PMID: 26539913 PMCID: PMC4670930 DOI: 10.1038/cddis.2015.323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 02/08/2023]
Abstract
Cyclopentenone prostaglandins (CyPGs), such as 15-deoxy-Δ12,14-prostaglandin J2 (15dPGJ2), are reactive prostaglandin metabolites exerting a variety of biological effects. CyPGs are produced in ischemic brain and disrupt the ubiquitin-proteasome system (UPS). Ubiquitin-C-terminal hydrolase L1 (UCH-L1) is a brain-specific deubiquitinating enzyme that has been linked to neurodegenerative diseases. Using tandem mass spectrometry (MS) analyses, we found that the C152 site of UCH-L1 is adducted by CyPGs. Mutation of C152 to alanine (C152A) inhibited CyPG modification and conserved recombinant UCH-L1 protein hydrolase activity after 15dPGJ2 treatment. A knock-in (KI) mouse expressing the UCH-L1 C152A mutation was constructed with the bacterial artificial chromosome (BAC) technique. Brain expression and distribution of UCH-L1 in the KI mouse was similar to that of wild type (WT) as determined by western blotting. Primary cortical neurons derived from KI mice were resistant to 15dPGJ2 cytotoxicity compared with neurons from WT mice as detected by the WST-1 cell viability assay and caspase-3 and poly ADP ribose polymerase (PARP) cleavage. This protective effect was accompanied with significantly less ubiquitinated protein accumulation and aggregation as well as less UCH-L1 aggregation in C152A KI primary neurons after 15dPGJ2 treatment. Additionally, 15dPGJ2-induced axonal injury was also significantly attenuated in KI neurons as compared with WT. Taken together, these studies indicate that UCH-L1 function is important in hypoxic neuronal death, and the C152 site of UCH-L1 has a significant role in neuronal survival after hypoxic/ischemic injury.
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Affiliation(s)
- H Liu
- Geriatric Research Educational and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.,Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - W Li
- Geriatric Research Educational and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.,Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - M E Rose
- Geriatric Research Educational and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.,Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - R W Hickey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - J Chen
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - G T Uechi
- Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Balasubramani
- Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA, USA
| | - B W Day
- Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - K V Patel
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - S H Graham
- Geriatric Research Educational and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.,Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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22
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Powis RA, Mutsaers CA, Wishart TM, Hunter G, Wirth B, Gillingwater TH. Increased levels of UCHL1 are a compensatory response to disrupted ubiquitin homeostasis in spinal muscular atrophy and do not represent a viable therapeutic target. Neuropathol Appl Neurobiol 2015; 40:873-87. [PMID: 25041530 DOI: 10.1111/nan.12168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/25/2014] [Indexed: 12/21/2022]
Abstract
AIM Levels of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) are robustly increased in spinal muscular atrophy (SMA) patient fibroblasts and mouse models. We therefore wanted to establish whether changes in UCHL1 contribute directly to disease pathogenesis, and to assess whether pharmacological inhibition of UCHL1 represents a viable therapeutic option for SMA. METHODS SMA mice and control littermates received a pharmacological UCHL1 inhibitor (LDN-57444) or DMSO vehicle. Survival and weight were monitored daily, a righting test of motor performance was performed, and motor neurone loss, muscle fibre atrophy and neuromuscular junction pathology were all quantified. Ubiquitin-like modifier activating enzyme 1 (Uba1) was then pharmacologically inhibited in neurones in vitro to examine the relationship between Uba1 levels and UCHL1 in SMA. RESULTS Pharmacological inhibition of UCHL1 failed to improve survival, motor symptoms or neuromuscular pathology in SMA mice and actually precipitated the onset of weight loss. LDN-57444 treatment significantly decreased spinal cord mono-ubiquitin levels, further exacerbating ubiquitination defects in SMA mice. Pharmacological inhibition of Uba1, levels of which are robustly reduced in SMA, was sufficient to induce accumulation of UCHL1 in primary neuronal cultures. CONCLUSION Pharmacological inhibition of UCHL1 exacerbates rather than ameliorates disease symptoms in a mouse model of SMA. Thus, pharmacological inhibition of UCHL1 is not a viable therapeutic target for SMA. Moreover, increased levels of UCHL1 in SMA likely represent a downstream consequence of decreased Uba1 levels, indicative of an attempted supportive compensatory response to defects in ubiquitin homeostasis caused by low levels of SMN protein.
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Affiliation(s)
- Rachael A Powis
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK; Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK
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23
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Nasheri N, Ning Z, Figeys D, Yao S, Goto NK, Pezacki JP. Activity-based profiling of the proteasome pathway during hepatitis C virus infection. Proteomics 2015; 15:3815-25. [PMID: 26314548 DOI: 10.1002/pmic.201500169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/28/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022]
Abstract
Hepatitis C virus (HCV) infection often leads to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The stability of the HCV proteins is controlled by ubiquitin-dependent and ubiquitin-independent proteasome pathways. Many viruses modulate proteasome function for their propagation. To examine the interrelationship between HCV and the proteasome pathways we employed a quantitative activity-based protein profiling method. Using this approach we were able to quantify the changes in the activity of several proteasome subunits and found that proteasome activity is drastically reduced by HCV replication. The results imply a link between the direct downregulation of the activity of this pathway and chronic HCV infection.
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Affiliation(s)
- Neda Nasheri
- Life Sciences Division, National Research Council of Canada, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Shao Yao
- Department of Chemistry, National University of Singapore, Singapore
| | - Natalie K Goto
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - John Paul Pezacki
- Life Sciences Division, National Research Council of Canada, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
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24
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Alonso-de Vega I, Martín Y, Smits VAJ. USP7 controls Chk1 protein stability by direct deubiquitination. Cell Cycle 2015; 13:3921-6. [PMID: 25483066 DOI: 10.4161/15384101.2014.973324] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chk1, an essential checkpoint kinase in the DNA damage response pathway (DDR), is tightly regulated by both ATR-dependent phosphorylation and proteasome-mediated degradation. Here we identify ubiquitin hydrolase USP7 as a novel regulator of Chk1 protein stability. USP7 was shown before to regulate other DDR proteins such as p53, Hdm2 and Claspin, an adaptor protein in the ATR-Chk1 pathway required for Chk1 activation. Depletion or inhibition of USP7 leads to lower Chk1 levels. The decreased Chk1 protein after USP7 knock down cannot be rescued by simultaneously elevating Claspin levels, demonstrating that the effect of USP7 on Chk1 is independent of its known effect on Claspin. Conversely, overexpression of USP7 wild type, but not a catalytic mutant version, elevates Chk1 levels and increases the half-life of Chk1 protein. Importantly, wild type, but not catalytic mutant USP7 can deubiquitinate Chk1 in vivo and in vitro, confirming that USP7 directly regulates Chk1 protein levels. Finally we show that USP7 catalytic mutant is (mono-)ubiquitinated, which suggests auto-deubiquitination by this ubiquitin hydrolase, possibly important for its regulation.
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Affiliation(s)
- Ignacio Alonso-de Vega
- a Unidad de Investigación ; Hospital Universitario de Canarias ; Instituto de Tecnologías Biomédicas ; Tenerife , Spain
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25
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Hanpude P, Bhattacharya S, Dey AK, Maiti TK. Deubiquitinating enzymes in cellular signaling and disease regulation. IUBMB Life 2015; 67:544-55. [PMID: 26178252 DOI: 10.1002/iub.1402] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 12/27/2022]
Abstract
Protein post-translational modification by ubiquitin represents a complex signaling system that regulates many cellular events including proteostasis to intercellular communications. Deubiquitinating enzymes (DUBs) that specifically disassemble Ub-chains or regulate ubiquitin homeostasis reside as a central component in ubiquitin signaling. Human genome encodes almost 100 DUBs and majority of them are not well characterized. Considerable progress has been made in the understanding of enzymatic mechanism; however, their cellular substrate specificity and regulation are largely unknown. Involvement of DUBs in disease regulation has been depicted since its discovery and several attempts have been made for evaluating DUBs as a drug target. In this review, we have updated briefly a new insight of DUBs activity, their cellular role, disease regulation, and therapeutic potential.
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Affiliation(s)
- Pranita Hanpude
- Laboratory of Proteomics and Cellular Signaling, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Bhakri Village, Faridabad, India
| | - Sushmita Bhattacharya
- Laboratory of Proteomics and Cellular Signaling, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Bhakri Village, Faridabad, India
| | - Amit Kumar Dey
- Laboratory of Proteomics and Cellular Signaling, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Bhakri Village, Faridabad, India
| | - Tushar Kanti Maiti
- Laboratory of Proteomics and Cellular Signaling, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Bhakri Village, Faridabad, India
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26
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Nakagawa T, Nakayama K. Protein monoubiquitylation: targets and diverse functions. Genes Cells 2015; 20:543-62. [PMID: 26085183 PMCID: PMC4744734 DOI: 10.1111/gtc.12250] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/19/2015] [Indexed: 12/14/2022]
Abstract
Ubiquitin is a 76-amino acid protein whose conjugation to protein targets is a form of post-translational modification. Protein ubiquitylation is characterized by the covalent attachment of the COOH-terminal carboxyl group of ubiquitin to an amino group of the substrate protein. Given that the NH2 -terminal amino group is usually masked, internal lysine residues are most often targeted for ubiquitylation. Polyubiquitylation refers to the formation of a polyubiquitin chain on the substrate as a result of the ubiquitylation of conjugated ubiquitin. The structures of such polyubiquitin chains depend on the specific lysine residues of ubiquitin targeted for ubiquitylation. Most of the polyubiquitin chains other than those linked via lysine-63 and methionine-1 of ubiquitin are recognized by the proteasome and serve as a trigger for substrate degradation. In contrast, polyubiquitin chains linked via lysine-63 and methionine-1 serve as a binding platform for proteins that function in immune signal transduction or DNA repair. With the exception of a few targets such as histones, the functions of protein monoubiquitylation have remained less clear. However, recent proteomics analysis has shown that monoubiquitylation occurs more frequently than polyubiquitylation, and studies are beginning to provide insight into its biologically important functions. Here, we summarize recent findings on protein monoubiquitylation to provide an overview of the targets and molecular functions of this modification.
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Affiliation(s)
- Tadashi Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, 980-8575, Miyagi, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, 980-8575, Miyagi, Japan
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Farshi P, Deshmukh RR, Nwankwo JO, Arkwright RT, Cvek B, Liu J, Dou QP. Deubiquitinases (DUBs) and DUB inhibitors: a patent review. Expert Opin Ther Pat 2015; 25:1191-1208. [PMID: 26077642 DOI: 10.1517/13543776.2015.1056737] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Deubiquitinating-enzymes (DUBs) are key components of the ubiquitin-proteasome system (UPS). The fundamental role of DUBs is specific removal of ubiquitin from substrates. DUBs contribute to activation/deactivation, recycling and localization of numerous regulatory proteins, and thus play major roles in diverse cellular processes. Altered DUB activity is associated with a multitudes of pathologies including cancer. Therefore, DUBs represent novel candidates for target-directed drug development. AREAS COVERED The article is a thorough review/accounting of patented compounds targeting DUBs and stratifying/classifying the patented compounds based on: chemical-structures, nucleic-acid compositions, modes-of-action, and targeting sites. The review provides a brief background on the UPS and the involvement of DUBs. Furthermore, methods for assessing efficacy and potential pharmacological utility of DUB inhibitor (DUBi) are discussed. EXPERT OPINION The FDA's approval of the 20S proteasome inhibitors (PIs): bortezomib and carfilzomib for treatment of hematological malignancies established the UPS as an anti-cancer target. Unfortunately, many patients are inherently resistant or develop resistance to PIs. One potential strategy to combat PI resistance is targeting upstream components of the UPS such as DUBs. DUBs represent a promising potential therapeutic target due to their critical roles in various cellular processes including protein turnover, localization and cellular homeostasis. While considerable efforts have been undertaken to develop DUB modulators, significant advancements are necessary to move DUBis into the clinic.
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Affiliation(s)
- Pershang Farshi
- Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Rahul R Deshmukh
- Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, Michigan, USA.,Department of Pathology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Joseph O Nwankwo
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Federal University, Ndufu-Alike Ikwo, Ebonyi State, Nigeria
| | - Richard T Arkwright
- Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, Michigan, USA.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Boris Cvek
- Department of Cell Biology & Genetics, Palacky University, Slechtitelu 11, Olomouc 78371, Czech Republic
| | - Jinbao Liu
- State Key Lab of Respiratory Disease, Protein Modification and Degradation Lab, Department of Pathophysiology, Guangzhou Medical University, Guangdong 510182, China
| | - Q Ping Dou
- Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, Michigan, USA.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan, USA.,Department of Pharmacology, School of Medicine, Wayne State University, Detroit, Michigan, USA.,Department of Pathology, School of Medicine, Wayne State University, Detroit, Michigan, USA
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28
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Sahtoe DD, Sixma TK. Layers of DUB regulation. Trends Biochem Sci 2015; 40:456-67. [PMID: 26073511 DOI: 10.1016/j.tibs.2015.05.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/06/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022]
Abstract
Proteolytic enzymes, such as (iso-)peptidases, are potentially hazardous for cells. To neutralize their potential danger, tight control of their activities has evolved. Deubiquitylating enzymes (DUBs) are isopeptidases involved in eukaryotic ubiquitylation. They reverse ubiquitin signals by hydrolyzing ubiquitin adducts, giving them control over all aspects of ubiquitin biology. The importance of DUB function is underscored by their frequent deregulation in human disease, making these enzymes potential drug targets. Here, we review the different layers of DUB enzyme regulation. We discuss how post-translational modification (PTM), regulatory domains within DUBs, and incorporation of DUBs into macromolecular complexes contribute to their activity. We conclude that most DUBs are likely to use a combination of these basic regulatory mechanisms.
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Affiliation(s)
- Danny D Sahtoe
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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Corsetti V, Florenzano F, Atlante A, Bobba A, Ciotti MT, Natale F, Della Valle F, Borreca A, Manca A, Meli G, Ferraina C, Feligioni M, D'Aguanno S, Bussani R, Ammassari-Teule M, Nicolin V, Calissano P, Amadoro G. NH2-truncated human tau induces deregulated mitophagy in neurons by aberrant recruitment of Parkin and UCHL-1: implications in Alzheimer's disease. Hum Mol Genet 2015; 24:3058-81. [PMID: 25687137 DOI: 10.1093/hmg/ddv059] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/10/2015] [Indexed: 01/26/2023] Open
Abstract
Disarrangement in functions and quality control of mitochondria at synapses are early events in Alzheimer's disease (AD) pathobiology. We reported that a 20-22 kDa NH2-tau fragment mapping between 26 and 230 amino acids of the longest human tau isoform (aka NH2htau): (i) is detectable in cellular and animal AD models, as well in synaptic mitochondria and cerebrospinal fluids (CSF) from human AD subjects; (ii) is neurotoxic in primary hippocampal neurons; (iii) compromises the mitochondrial biology both directly, by inhibiting the ANT-1-dependent ADP/ATP exchange, and indirectly, by impairing their selective autophagic clearance (mitophagy). Here, we show that the extensive Parkin-dependent turnover of mitochondria occurring in NH2htau-expressing post-mitotic neurons plays a pro-death role and that UCHL-1, the cytosolic Ubiquitin-C-terminal hydrolase L1 which directs the physiological remodeling of synapses by controlling ubiquitin homeostasis, critically contributes to mitochondrial and synaptic failure in this in vitro AD model. Pharmacological or genetic suppression of improper mitophagy, either by inhibition of mitochondrial targeting to autophagosomes or by shRNA-mediated silencing of Parkin or UCHL-1 gene expression, restores synaptic and mitochondrial content providing partial but significant protection against the NH2htau-induced neuronal death. Moreover, in mitochondria from human AD synapses, the endogenous NH2htau is stably associated with Parkin and with UCHL-1. Taken together, our studies show a causative link between the excessive mitochondrial turnover and the NH2htau-induced in vitro neuronal death, suggesting that pathogenetic tau truncation may contribute to synaptic deterioration in AD by aberrant recruitment of Parkin and UCHL-1 to mitochondria making them more prone to detrimental autophagic clearance.
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Affiliation(s)
- V Corsetti
- Institute of Translational Pharmacology (IFT) - National Research Council (CNR), Via Fosso del Cavaliere 100-00133, Rome, Italy
| | - F Florenzano
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - A Atlante
- Institute of Biomembranes and Bioenergetics (IBBE)-CNR, Via Amendola 165/A, 70126 Bari, Italy
| | - A Bobba
- Institute of Biomembranes and Bioenergetics (IBBE)-CNR, Via Amendola 165/A, 70126 Bari, Italy
| | - M T Ciotti
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - F Natale
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - F Della Valle
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - A Borreca
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - A Manca
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - G Meli
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - C Ferraina
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - M Feligioni
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - S D'Aguanno
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - R Bussani
- UCO Pathological Anatomy and Histopathology Unit, Cattinara Hospital Strada di Fiume 447, 34149 Trieste, Italy and
| | - M Ammassari-Teule
- Institute of Cellular Biology and Neuroscience (IBCN)-CNR, IRCSS Santa Lucia Foundation Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - V Nicolin
- Department of Medical, Surgical and Health Science, University of Trieste, Strada di Fiume 449, 34149 Trieste, Italy
| | - P Calissano
- European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
| | - G Amadoro
- Institute of Translational Pharmacology (IFT) - National Research Council (CNR), Via Fosso del Cavaliere 100-00133, Rome, Italy European Brain Research Institute (EBRI), Via del Fosso di Fiorano 64-65, 00143 Rome, Italy
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30
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McKeon JE, Sha D, Li L, Chin LS. Parkin-mediated K63-polyubiquitination targets ubiquitin C-terminal hydrolase L1 for degradation by the autophagy-lysosome system. Cell Mol Life Sci 2014; 72:1811-24. [PMID: 25403879 DOI: 10.1007/s00018-014-1781-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/04/2014] [Accepted: 11/13/2014] [Indexed: 11/24/2022]
Abstract
Ubiquitin C-terminal hydrolase L1 (UCH-L1) is a key neuronal deubiquitinating enzyme which is mutated in Parkinson disease (PD) and in childhood-onset neurodegenerative disorder with optic atrophy. Furthermore, reduced UCH-L1 protein levels are associated with a number of neurodegenerative diseases, whereas up-regulation of UCH-L1 protein expression is found in multiple types of cancer. However, very little is known about how UCH-L1 protein level is regulated in cells. Here, we report that UCH-L1 is a novel interactor and substrate of PD-linked E3 ubiquitin-protein ligase parkin. We find that parkin mediates K63-linked polyubiquitination of UCH-L1 in cooperation with the Ubc13/Uev1a E2 ubiquitin-conjugating enzyme complex and promotes UCH-L1 degradation by the autophagy-lysosome pathway. Targeted disruption of parkin gene expression in mice causes a significant decrease in UCH-L1 ubiquitination with a concomitant increase in UCH-L1 protein level in brain, supporting an in vivo role of parkin in regulating UCH-L1 ubiquitination and degradation. Our findings reveal a direct link between parkin-mediated ubiquitin signaling and UCH-L1 regulation, and they have important implications for understanding the roles of these two proteins in health and disease.
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Affiliation(s)
- Jeanne E McKeon
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, 30322, USA
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Bishop P, Rubin P, Thomson AR, Rocca D, Henley JM. The ubiquitin C-terminal hydrolase L1 (UCH-L1) C terminus plays a key role in protein stability, but its farnesylation is not required for membrane association in primary neurons. J Biol Chem 2014; 289:36140-9. [PMID: 25326379 PMCID: PMC4276877 DOI: 10.1074/jbc.m114.557124] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin C-terminal hydrolase L1 (UCH-L1) is a deubiquitinating enzyme that is highly expressed in neurons. A possible role for UCH-L1 in neurodegeneration has been highlighted because of its presence in Lewy bodies associated with Parkinson disease and neurofibrillary tangles observed in Alzheimer disease. UCH-L1 exists in two forms in neurons, a soluble cytoplasmic form (UCH-L1(C)) and a membrane-associated form (UCH-L1(M)). Alzheimer brains show reduced levels of soluble UCH-L1(C) correlating with the formation of UCH-L1-immunoreactive tau tangles, whereas UCH-L1(M) has been implicated in α-synuclein dysfunction. Given these reports of divergent roles, we investigated the properties of UCH-L1 membrane association. Surprisingly, our results indicate that UCH-L1 does not partition to the membrane in the cultured cell lines we tested. Furthermore, in primary cultured neurons, a proportion of UCH-L1(M) does partition to the membrane, but, contrary to a previous report, this does not require farnesylation. Deletion of the four C-terminal residues caused the loss of protein solubility, abrogation of substrate binding, increased cell death, and an abnormal intracellular distribution, consistent with protein dysfunction and aggregation. These data indicate that UCH-L1 is differently processed in neurons compared with clonal cell lines and that farnesylation does not account for the membrane association in neurons.
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Affiliation(s)
- Paul Bishop
- From the School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Philip Rubin
- From the School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Andrew R Thomson
- From the School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Dan Rocca
- From the School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jeremy M Henley
- From the School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
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Charbonneau ME, Gonzalez-Hernandez MJ, Showalter HD, Donato NJ, Wobus CE, O’Riordan MXD. Small molecule deubiquitinase inhibitors promote macrophage anti-infective capacity. PLoS One 2014; 9:e104096. [PMID: 25093325 PMCID: PMC4122495 DOI: 10.1371/journal.pone.0104096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/07/2014] [Indexed: 12/18/2022] Open
Abstract
The global spread of anti-microbial resistance requires urgent attention, and diverse alternative strategies have been suggested to address this public health concern. Host-directed immunomodulatory therapies represent one approach that could reduce selection for resistant bacterial strains. Recently, the small molecule deubiquitinase inhibitor WP1130 was reported as a potential anti-infective drug against important human food-borne pathogens, notably Listeria monocytogenes and noroviruses. Utilization of WP1130 itself is limited due to poor solubility, but given the potential of this new compound, we initiated an iterative rational design approach to synthesize new derivatives with increased solubility that retained anti-infective activity. Here, we test a small library of novel synthetic molecules based on the structure of the parent compound, WP1130, for anti-infective activity in vitro. Our studies identify a promising candidate, compound 9, which reduced intracellular growth of L. monocytogenes at concentrations that caused minimal cellular toxicity. Compound 9 itself had no bactericidal activity and only modestly slowed Listeria growth rate in liquid broth culture, suggesting that this drug acts as an anti-infective compound by modulating host-cell function. Moreover, this new compound also showed anti-infective activity against murine norovirus (MNV-1) and human norovirus, using the Norwalk virus replicon system. This small molecule inhibitor may provide a chemical platform for further development of therapeutic deubiquitinase inhibitors with broad-spectrum anti-infective activity.
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Affiliation(s)
- Marie-Eve Charbonneau
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marta J. Gonzalez-Hernandez
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Hollis D. Showalter
- Vahlteich Medicinal Chemistry Core, Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas J. Donato
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mary X. D. O’Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Chen P, Parmalee N, Aschner M. Genetic factors and manganese-induced neurotoxicity. Front Genet 2014; 5:265. [PMID: 25136353 PMCID: PMC4120679 DOI: 10.3389/fgene.2014.00265] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/18/2014] [Indexed: 11/13/2022] Open
Abstract
Manganese (Mn), is a trace metal required for normal physiological processes in humans. Mn levels are tightly regulated, as high levels of Mn result in accumulation in the brain and cause a neurological disease known as manganism. Manganism shares many similarities with Parkinson’s disease (PD), both at the physiological level and the cellular level. Exposure to high Mn-containing environments increases the risk of developing manganism. Mn is absorbed primarily through the intestine and then released in the blood. Excessive Mn is secreted in the bile and excreted in feces. Mn enters and exits cells through a number of non-specific importers localized on the cell membrane. Mutations in one of the Mn exporters, SLC30A10 (solute carrier family 30, member 10), result in Mn induced toxicity with liver impairments and neurological dysfunction. Four PD genes have been identified in connection to regulation of Mn toxicity, shedding new light on potential links between manganism and PD.
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Affiliation(s)
- Pan Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine Bronx, NY, USA
| | - Nancy Parmalee
- Department of Molecular Pharmacology, Albert Einstein College of Medicine Bronx, NY, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine Bronx, NY, USA
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van Loosdregt J, Coffer PJ. Post-translational modification networks regulating FOXP3 function. Trends Immunol 2014; 35:368-78. [PMID: 25047417 DOI: 10.1016/j.it.2014.06.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 06/23/2014] [Accepted: 06/23/2014] [Indexed: 01/01/2023]
Abstract
Forkhead box (FOX)P3 is a requisite transcription factor for the development and maintenance of immunosuppressive function of regulatory T (Treg) cells, and therefore for immune homeostasis. Post-translational modifications (PTMs) can transiently alter the functionality of transcription factors, and recent evidence reveals that FOXP3 can be regulated by various PTMs including acetylation, ubiquitination, and phosphorylation. Here, we review the current understanding of how these modifications control FOXP3, including regulation of DNA binding, transactivation potential, and proteasomal degradation. We place these findings in the context of the biology of Treg cells, and discuss both limitations in translating biochemical findings into in vivo functions and the opportunities presented by a better understanding of the molecular mechanisms that can transiently control FOXP3 activity in response to environmental cues.
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Affiliation(s)
- Jorg van Loosdregt
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul J Coffer
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands; Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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35
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Kim HJ, Kim HJ, Jeong JE, Baek JY, Jeong J, Kim S, Kim YM, Kim Y, Nam JH, Huh SH, Seo J, Jin BK, Lee KJ. N-terminal truncated UCH-L1 prevents Parkinson's disease associated damage. PLoS One 2014; 9:e99654. [PMID: 24959670 PMCID: PMC4069018 DOI: 10.1371/journal.pone.0099654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/16/2014] [Indexed: 11/20/2022] Open
Abstract
Ubiquitin C-terminal hydrolase-L1 (UCH-L1) has been proposed as one of the Parkinson's disease (PD) related genes, but the possible molecular connection between UCH-L1 and PD is not well understood. In this study, we discovered an N-terminal 11 amino acid truncated variant UCH-L1 that we called NT-UCH-L1, in mouse brain tissue as well as in NCI-H157 lung cancer and SH-SY5Y neuroblastoma cell lines. In vivo experiments and hydrogen-deuterium exchange (HDX) with tandem mass spectrometry (MS) studies showed that NT-UCH-L1 is readily aggregated and degraded, and has more flexible structure than UCH-L1. Post-translational modifications including monoubiquitination and disulfide crosslinking regulate the stability and cellular localization of NT-UCH-L1, as confirmed by mutational and proteomic studies. Stable expression of NT-UCH-L1 decreases cellular ROS levels and protects cells from H2O2, rotenone and CCCP-induced cell death. NT-UCH-L1-expressing transgenic mice are less susceptible to degeneration of nigrostriatal dopaminergic neurons seen in the MPTP mouse model of PD, in comparison to control animals. These results suggest that NT-UCH-L1 may have the potential to prevent neural damage in diseases like PD.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Hyun Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jae-Eun Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jeong Yeob Baek
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Sun Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Young-Mee Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Youhwa Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Jin Han Nam
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Sue Hee Huh
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Jawon Seo
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Byung Kwan Jin
- Department of Biochemistry and Molecular Biology, Neurodegeneration Control Research Center, School of Medicine, Kyung Hee University, Seoul, Korea
- * E-mail: (KJL); (BKJ)
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea
- * E-mail: (KJL); (BKJ)
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Contu VR, Kotake Y, Toyama T, Okuda K, Miyara M, Sakamoto S, Samizo S, Sanoh S, Kumagai Y, Ohta S. Endogenous neurotoxic dopamine derivative covalently binds to Parkinson's disease-associated ubiquitin C-terminal hydrolase L1 and alters its structure and function. J Neurochem 2014; 130:826-38. [DOI: 10.1111/jnc.12762] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Viorica Raluca Contu
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Yaichiro Kotake
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Takashi Toyama
- Graduate School of Comprehensive Human Sciences; University of Tsukuba; Tsukuba Japan
| | - Katsuhiro Okuda
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Masatsugu Miyara
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Shuichiro Sakamoto
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Shigeyoshi Samizo
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Seigo Sanoh
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Yoshito Kumagai
- Graduate School of Comprehensive Human Sciences; University of Tsukuba; Tsukuba Japan
| | - Shigeru Ohta
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
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Mashtalir N, Daou S, Barbour H, Sen N, Gagnon J, Hammond-Martel I, Dar H, Therrien M, Affar E. Autodeubiquitination Protects the Tumor Suppressor BAP1 from Cytoplasmic Sequestration Mediated by the Atypical Ubiquitin Ligase UBE2O. Mol Cell 2014; 54:392-406. [DOI: 10.1016/j.molcel.2014.03.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 01/21/2014] [Accepted: 02/13/2014] [Indexed: 11/26/2022]
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38
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Could dysregulation of UPS be a common underlying mechanism for cancer and neurodegeneration? Lessons from UCHL1. Cell Biochem Biophys 2014; 67:45-53. [PMID: 23695785 DOI: 10.1007/s12013-013-9631-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ubiquitin proteasome system (UPS) determines the timing and extent of protein turnover in cells, and it is one of the most strictly controlled cellular mechanisms. Lack of proper control over UPS is attributed to both cancer and to neurodegenerative diseases, yet in different context and direction. Cancerous cells have altered cellular metabolisms, uncontrolled cellular division, and increased proteasome activity. The specialized function prevent neurons from undergoing cellular division but allow them to extend an axon over long distances, establish connections, and to form stable neuronal circuitries. Neurons heavily depend on the proper function of the proteasome and the UPS for their proper function. Reduction of UPS function in vulnerable neurons results in protein aggregation, increased ER stress, and cell death. Identification of compounds that selectively block proteasome function in distinct set of malignancies added momentum to drug discovery efforts, and deubiquitinases (DUBs) gained much attention. This review will focus on ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a DUB that is attributed to both cancer and neurodegeneration. The potential of developing effective treatment strategies for two major health problems by controlling the function of UPS opens up new avenues for innovative approaches and therapeutic interventions.
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Villamil MA, Liang Q, Zhuang Z. The WD40-repeat protein-containing deubiquitinase complex: catalysis, regulation, and potential for therapeutic intervention. Cell Biochem Biophys 2014; 67:111-26. [PMID: 23797609 DOI: 10.1007/s12013-013-9637-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ubiquitination has emerged as an essential signaling mechanism in eukaryotes. Deubiquitinases (DUBs) counteract the activities of the ubiquitination machinery and provide another level of control in cellular ubiquitination. Not surprisingly, DUBs are subjected to stringent regulations. Besides regulation by the noncatalytic domains present in the DUB sequences, DUB-interacting proteins are increasingly realized as essential regulators for DUB activity and function. This review focuses on DUBs that are associated with WD40-repeat proteins. Many human ubiquitin-specific proteases (USPs) were found to interact with WD40-repeat proteins, but little is known as to how this interaction regulates the activity and function of USPs. In recent years, significant progress has been made in understanding a prototypical WD40-repeat protein-containing DUB complex that comprises USP1 and USP1-associated factor 1 (UAF1). It has been shown that UAF1 activates USP1 through a potential active-site modulation, and the complex formation between USP1 and UAF1 is regulated by serine phosphorylation. Recently, human USPs have been recognized as a promising target class for inhibitor discovery. Small molecule inhibitors targeting several human USPs have been reported. USP1 is involved in two major DNA damage response pathways, DNA translesion synthesis and the Fanconi anemia pathway. Inhibiting the USP1/UAF1 deubiquitinase complex represents a new strategy to potentiate cancer cells to DNA-crosslinking agents and to overcome resistance that has plagued clinical cancer chemotherapy. The progress in inhibitor discovery against USPs and the WD40-repeat protein-containing USP complex will be discussed.
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Affiliation(s)
- Mark A Villamil
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
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van Loosdregt J, Fleskens V, Fu J, Brenkman AB, Bekker CPJ, Pals CEGM, Meerding J, Berkers CR, Barbi J, Gröne A, Sijts AJAM, Maurice MM, Kalkhoven E, Prakken BJ, Ovaa H, Pan F, Zaiss DMW, Coffer PJ. Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity 2013; 39:259-71. [PMID: 23973222 DOI: 10.1016/j.immuni.2013.05.018] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 05/06/2013] [Indexed: 11/18/2022]
Abstract
Stable Foxp3 expression is required for the development of functional regulatory T (Treg) cells. Here, we demonstrate that the expression of the transcription factor Foxp3 can be regulated through the polyubiquitination of multiple lysine residues, resulting in proteasome-mediated degradation. Expression of the deubiquitinase (DUB) USP7 was found to be upregulated and active in Treg cells, being associated with Foxp3 in the nucleus. Ectopic expression of USP7 decreased Foxp3 polyubiquitination and increased Foxp3 expression. Conversely, either treatment with DUB inhibitor or USP7 knockdown decreased endogenous Foxp3 protein expression and decreased Treg-cell-mediated suppression in vitro. Furthermore, in a murine adoptive-transfer-induced colitis model, either inhibition of DUB activity or USP7 knockdown in Treg cells abrogated their ability to resolve inflammation in vivo. Our data reveal a molecular mechanism in which rapid temporal control of Foxp3 expression in Treg cells can be regulated by USP7, thereby modulating Treg cell numbers and function.
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Affiliation(s)
- Jorg van Loosdregt
- Department of Immunology, University Medical Center Utrecht, Utrecht 3584EA, The Netherlands
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Tsou WL, Burr AA, Ouyang M, Blount JR, Scaglione KM, Todi SV. Ubiquitination regulates the neuroprotective function of the deubiquitinase ataxin-3 in vivo. J Biol Chem 2013; 288:34460-9. [PMID: 24106274 DOI: 10.1074/jbc.m113.513903] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Deubiquitinases (DUBs) are proteases that regulate various cellular processes by controlling protein ubiquitination. Cell-based studies indicate that the regulation of the activity of DUBs is important for homeostasis and is achieved by multiple mechanisms, including through their own ubiquitination. However, the physiological significance of the ubiquitination of DUBs to their functions in vivo is unclear. Here, we report that ubiquitination of the DUB ataxin-3 at lysine residue 117, which markedly enhances its protease activity in vitro, is critical for its ability to suppress toxic protein-dependent degeneration in Drosophila melanogaster. Compared with ataxin-3 with only Lys-117 present, ataxin-3 that does not become ubiquitinated performs significantly less efficiently in suppressing or delaying the onset of toxic protein-dependent degeneration in flies. According to further studies, the C terminus of Hsc70-interacting protein (CHIP), an E3 ubiquitin ligase that ubiquitinates ataxin-3 in vitro, is dispensable for its ubiquitination in vivo and is not required for the neuroprotective function of this DUB in Drosophila. Our work also suggests that ataxin-3 suppresses degeneration by regulating toxic protein aggregation rather than stability.
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Affiliation(s)
- Wei-Ling Tsou
- From the Departments of Pharmacology and Neurology and
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Sosna J, Voigt S, Mathieu S, Kabelitz D, Trad A, Janssen O, Meyer-Schwesinger C, Schütze S, Adam D. The proteases HtrA2/Omi and UCH-L1 regulate TNF-induced necroptosis. Cell Commun Signal 2013; 11:76. [PMID: 24090154 PMCID: PMC3850939 DOI: 10.1186/1478-811x-11-76] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/01/2013] [Indexed: 11/23/2022] Open
Abstract
Background In apoptosis, proteolysis by caspases is the primary mechanism for both initiation and execution of programmed cell death (PCD). In contrast, the impact of proteolysis on the regulation and execution of caspase-independent forms of PCD (programmed necrosis, necroptosis) is only marginally understood. Likewise, the identity of the involved proteases has remained largely obscure. Here, we have investigated the impact of proteases in TNF-induced necroptosis. Results The serine protease inhibitor TPKC protected from TNF-induced necroptosis in multiple murine and human cells systems whereas inhibitors of metalloproteinases or calpain/cysteine and cathepsin proteases had no effect. A screen for proteins labeled by a fluorescent TPCK derivative in necroptotic cells identified HtrA2/Omi (a serine protease previously implicated in PCD) as a promising candidate. Demonstrating its functional impact, pharmacological inhibition or genetic deletion of HtrA2/Omi protected from TNF-induced necroptosis. Unlike in apoptosis, HtrA2/Omi did not cleave another protease, ubiquitin C-terminal hydrolase (UCH-L1) during TNF-induced necroptosis, but rather induced monoubiquitination indicative for UCH-L1 activation. Correspondingly, pharmacologic or RNA interference-mediated inhibition of UCH-L1 protected from TNF-induced necroptosis. We found that UCH-L1 is a mediator of caspase-independent, non-apoptotic cell death also in diseased kidney podocytes by measuring cleavage of the protein PARP-1, caspase activity, cell death and cell morphology. Indicating a role of TNF in this process, podocytes with stably downregulated UCH-L1 proved resistant to TNF-induced necroptosis. Conclusions The proteases HtrA2/Omi and UCH-L1 represent two key components of TNF-induced necroptosis, validating the relevance of proteolysis not only for apoptosis, but also for caspase-independent PCD. Since UCH-L1 clearly contributes to the non-apoptotic death of podocytes, interference with the necroptotic properties of HtrA2/Omi and UCH-L1 may prove beneficial for the treatment of patients, e.g. in kidney failure.
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Affiliation(s)
- Justyna Sosna
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Michaelisstr, 5, 24105 Kiel, Germany.
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Frisan T, Coppotelli G, Dryselius R, Masucci MG. Ubiquitin C-terminal hydrolase-L1 interacts with adhesion complexes and promotes cell migration, survival, and anchorage independent growth. FASEB J 2012; 26:5060-70. [PMID: 22932395 DOI: 10.1096/fj.12-211946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ubiquitin C-terminal hydrolase-L1 (UCH-L1) is a deubiquitinating enzyme of unknown function that is highly expressed in neurons and overexpressed in several human cancers. UCH-L1 has been implicated in the regulation of phenotypic properties associated with malignant cell growth but the underlying mechanisms have not been elucidated. By comparing cells expressing catalytically active or inactive versions of UCH-L1, we found that the active enzyme enhances cell adhesion, spreading, and migration; inhibits anoikis; and promotes anchorage independent growth. UCH-L1 accumulates at the motile edge of the cell membrane during the initial phases of adhesion, colocalizes with focal adhesion kinase (FAK), p120-catenin, and vinculin, and enhances the formation of focal adhesions, which correlates with enhanced FAK activation. The involvement of UCH-L1 in the regulation of focal adhesions and adherens junctions is supported by coimmunoprecipitation with key components of these complexes, including FAK, paxillin, p120-catenin, β-catenin, and vinculin. UCH-L1 stabilizes focal adhesion signaling in the absence of adhesion, as assessed by reduced caspase-dependent cleavage of FAK following cell detachment and sustained activity of the AKT signaling pathway. These findings offer new insights on the molecular interactions through which the deubiquitinating enzyme regulates the survival, proliferation, and metastatic potential of malignant cells.
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Affiliation(s)
- Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden, Box 285, S-171 77 Stockholm, Sweden
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Xiang T, Li L, Yin X, Yuan C, Tan C, Su X, Xiong L, Putti TC, Oberst M, Kelly K, Ren G, Tao Q. The ubiquitin peptidase UCHL1 induces G0/G1 cell cycle arrest and apoptosis through stabilizing p53 and is frequently silenced in breast cancer. PLoS One 2012; 7:e29783. [PMID: 22279545 PMCID: PMC3261155 DOI: 10.1371/journal.pone.0029783] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/05/2011] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer (BrCa) is a complex disease driven by aberrant gene alterations and environmental factors. Recent studies reveal that abnormal epigenetic gene regulation also plays an important role in its pathogenesis. Ubiquitin carboxyl- terminal esterase L1 (UCHL1) is a tumor suppressor silenced by promoter methylation in multiple cancers, but its role and alterations in breast tumorigenesis remain unclear. Methodology/Principal Findings We found that UCHL1 was frequently downregulated or silenced in breast cancer cell lines and tumor tissues, but readily expressed in normal breast tissues and mammary epithelial cells. Promoter methylation of UCHL1 was detected in 9 of 10 breast cancer cell lines (90%) and 53 of 66 (80%) primary tumors, but rarely in normal breast tissues, which was statistically correlated with advanced clinical stage and progesterone receptor status. Pharmacologic demethylation reactivated UCHL1 expression along with concomitant promoter demethylation. Ectopic expression of UCHL1 significantly suppressed the colony formation and proliferation of breast tumor cells, through inducing G0/G1 cell cycle arrest and apoptosis. Subcellular localization study showed that UCHL1 increased cytoplasmic abundance of p53. We further found that UCHL1 induced p53 accumulation and reduced MDM2 protein level, and subsequently upregulated the expression of p21, as well as cleavage of caspase3 and PARP, but not in catalytic mutant UCHL1 C90S-expressed cells. Conclusions/Significance UCHL1 exerts its tumor suppressive functions by inducing G0/G1cell cycle arrest and apoptosis in breast tumorigenesis, requiring its deubiquitinase activity. Its frequent silencing by promoter CpG methylation may serve as a potential tumor marker for breast cancer.
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Affiliation(s)
- Tingxiu Xiang
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xuedong Yin
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chenfu Yuan
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Cui Tan
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianwei Su
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Lei Xiong
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas C. Putti
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michael Oberst
- Signal Transduction Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathleen Kelly
- Signal Transduction Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guosheng Ren
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- * E-mail: (GR); (QT)
| | - Qian Tao
- Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (GR); (QT)
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Abstract
The assay of the activity of ubiquitin (Ub) ligases (E3s) and screens for pharmacological agents that alter their function are a continual challenge for basic investigators as well as in drug development. The assay of different E3s requires distinct detection methods and reagents (e.g., specific antibodies against each E3 or substrate). So, a single assay applicable to many E3s could be very useful. Here, we demonstrate that S5a/Rpn10 binds to the growing polyUb chain formed on a substrate (or on the Ub ligase during autoubiquitination) and then itself becomes extensively ubiquitinated. S5a thus can serve as a universal substrate for ubiquitination. This biochemical property of S5a provides a method for measuring the enzymatic activity of any E3. This approach is valuable when substrates are not known or not available and when multiple ubiquitination reactions are being studied (e.g., in high-throughput screens).
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Affiliation(s)
- Hyoung Tae Kim
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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Kang C, Yi GS. Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs. BMC Bioinformatics 2011; 12 Suppl 14:S8. [PMID: 22373085 PMCID: PMC3287473 DOI: 10.1186/1471-2105-12-s14-s8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs. Results We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods. Conclusions This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra.
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Affiliation(s)
- Chiyong Kang
- Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, South Korea
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Kessler BM, Edelmann MJ. PTMs in conversation: activity and function of deubiquitinating enzymes regulated via post-translational modifications. Cell Biochem Biophys 2011; 60:21-38. [PMID: 21480003 PMCID: PMC3094536 DOI: 10.1007/s12013-011-9176-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deubiquitinating enzymes (DUBs) constitute a diverse protein family and their impact on numerous biological and pathological processes has now been widely appreciated. Many DUB functions have to be tightly controlled within the cell, and this can be achieved in several ways, such as substrate-induced conformational changes, binding to adaptor proteins, proteolytic cleavage, and post-translational modifications (PTMs). This review is focused on the role of PTMs including monoubiquitination, sumoylation, acetylation, and phosphorylation as characterized and putative regulative factors of DUB function. Although this aspect of DUB functionality has not been yet thoroughly studied, PTMs represent a versatile and reversible method of controlling the role of DUBs in biological processes. In several cases PTMs might constitute a feedback mechanism insuring proper functioning of the ubiquitin proteasome system and other DUB-related pathways.
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Affiliation(s)
- Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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48
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Fraile JM, Quesada V, Rodríguez D, Freije JMP, López-Otín C. Deubiquitinases in cancer: new functions and therapeutic options. Oncogene 2011; 31:2373-88. [PMID: 21996736 DOI: 10.1038/onc.2011.443] [Citation(s) in RCA: 330] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Deubiquitinases (DUBs) have fundamental roles in the ubiquitin system through their ability to specifically deconjugate ubiquitin from targeted proteins. The human genome encodes at least 98 DUBs, which can be grouped into 6 families, reflecting the need for specificity in their function. The activity of these enzymes affects the turnover rate, activation, recycling and localization of multiple proteins, which in turn is essential for cell homeostasis, protein stability and a wide range of signaling pathways. Consistent with this, altered DUB function has been related to several diseases, including cancer. Thus, multiple DUBs have been classified as oncogenes or tumor suppressors because of their regulatory functions on the activity of other proteins involved in tumor development. Therefore, recent studies have focused on pharmacological intervention on DUB activity as a rationale to search for novel anticancer drugs. This strategy may benefit from our current knowledge of the physiological regulatory mechanisms of these enzymes and the fact that growth of several tumors depends on the normal activity of certain DUBs. Further understanding of these processes may provide answers to multiple remaining questions on DUB functions and lead to the development of DUB-targeting strategies to expand the repertoire of molecular therapies against cancer.
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Affiliation(s)
- J M Fraile
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
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Weissman AM, Shabek N, Ciechanover A. The predator becomes the prey: regulating the ubiquitin system by ubiquitylation and degradation. Nat Rev Mol Cell Biol 2011; 12:605-20. [PMID: 21860393 PMCID: PMC3545438 DOI: 10.1038/nrm3173] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ubiquitylation (also known as ubiquitination) regulates essentially all of the intracellular processes in eukaryotes through highly specific modification of numerous cellular proteins, which is often tightly regulated in a spatial and temporal manner. Although most often associated with proteasomal degradation, ubiquitylation frequently serves non-proteolytic functions. In light of its central roles in cellular regulation, it has not been surprising to find that many of the components of the ubiquitin system itself are regulated by ubiquitylation. This observation has broad implications for pathophysiology.
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Affiliation(s)
- Allan M. Weissman
- Laboratory of Protein Dynamics and Signaling, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nitzan Shabek
- Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Aaron Ciechanover
- Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Autocatalytic activity of the ubiquitin-specific protease domain of herpes simplex virus 1 VP1-2. J Virol 2011; 85:8738-51. [PMID: 21715485 DOI: 10.1128/jvi.00798-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The herpes simplex virus (HSV) tegument protein VP1-2 is essential for virus entry and assembly. VP1-2 also contains a highly conserved ubiquitin-specific protease (USP) domain within its N-terminal region. Despite conservation of the USP and the demonstration that it can act on artificial substrates such as polyubiquitin chains, identification of the relevance of the USP in vivo to levels or function of any substrate remains limited. Here we show that HSV VP1-2 USP can act on itself and is important for stability. VP1-2 N-terminal variants encompassing the core USP domain itself were not affected by mutation of the catalytic cysteine residue (C65). However, extending the N-terminal region resulted in protein species requiring USP activity for accumulation. In this context, C65A mutation resulted in a drastic reduction in protein levels which could be stabilized by proteosomal inhibition or by the presence of normal C65. The functional USP domain could increase abundance of unstable variants, indicating action at least in part, in trans. Interestingly, full-length variants containing the inactive USP, although unstable when expressed in isolation, were stabilized by virus infection. The catalytically inactive VP1-2 retained complementation activity of a VP1-2-negative virus. Furthermore, a recombinant virus expressing a C65A mutant VP1-2 exhibited little difference in single-step growth curves and the kinetics and abundance of VP1-2 or a number of test proteins. Despite the absence of a phenotype for these replication parameters, the USP activity of VP1-2 may be required for function, including its own stability, under certain circumstances.
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