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Gorka M, Magnussen HM, Kulathu Y. Chemical biology tools to study Deubiquitinases and Ubl proteases. Semin Cell Dev Biol 2022; 132:86-96. [PMID: 35216867 DOI: 10.1016/j.semcdb.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
The reversible attachment of ubiquitin (Ub) and ubiquitin like modifiers (Ubls) to proteins are crucial post-translational modifications (PTMs) for many cellular processes. Not only do cells possess hundreds of ligases to mediate substrate specific modification with Ub and Ubls, but they also have a repertoire of more than 100 dedicated enzymes for the specific removal of ubiquitin (Deubiquitinases or DUBs) and Ubl modifications (Ubl-specific proteases or ULPs). Over the past two decades, there has been significant progress in our understanding of how DUBs and ULPs function at a molecular level and many novel DUBs and ULPs, including several new DUB classes, have been identified. Here, the development of chemical tools that can bind and trap active DUBs has played a key role. Since the introduction of the first activity-based probe for DUBs in 1986, several innovations have led to the development of more sophisticated tools to study DUBs and ULPs. In this review we discuss how chemical biology has led to the development of activity-based probes and substrates that have been invaluable to the study of DUBs and ULPs. We summarise our currently available toolbox, highlight the main achievements and give an outlook of how these tools may be applied to gain a better understanding of the regulatory mechanisms of DUBs and ULPs.
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Affiliation(s)
- Magdalena Gorka
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Helge Magnus Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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2
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TIFAB Regulates USP15-Mediated p53 Signaling during Stressed and Malignant Hematopoiesis. Cell Rep 2021; 30:2776-2790.e6. [PMID: 32101751 PMCID: PMC7384867 DOI: 10.1016/j.celrep.2020.01.093] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2019] [Accepted: 01/24/2020] [Indexed: 12/16/2022] Open
Abstract
TRAF-interacting protein with a forkhead-associated domain B (TIFAB) is implicated in myeloid malignancies with deletion of chromosome 5q. Employing a combination of proteomic and genetic approaches, we find that TIFAB regulates ubiquitin-specific peptidase 15 (USP15) ubiquitin hydrolase activity. Expression of TIFAB in hematopoietic stem/progenitor cells (HSPCs) permits USP15 signaling to substrates, including MDM2 and KEAP1, and mitigates p53 expression. Consequently, TIFAB-deficient HSPCs exhibit compromised USP15 signaling and are sensitized to hematopoietic stress by derepression of p53. In MLL-AF9 leukemia, deletion of TIFAB increases p53 signaling and correspondingly decreases leukemic cell function and development of leukemia. Restoring USP15 expression partially rescues the function of TIFAB-deficient MLL-AF9 cells. Conversely, elevated TIFAB represses p53, increases leukemic progenitor function, and correlates with MLL gene expression programs in leukemia patients. Our studies uncover a function of TIFAB as an effector of USP15 activity and rheostat of p53 signaling in stressed and malignant HSPCs. Niederkorn et al. identify TIFAB as a critical node in hematopoietic cells under stressed and oncogenic cell states. Their studies indicate that deregulation of the TIFAB-USP15 complex, as observed in del(5q) myelodysplasia or MLL-rearranged leukemia, modulates p53 activity and has critical functional consequences for stressed and malignant hematopoietic cells.
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3
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Gui W, Shen S, Zhuang Z. Photocaged Cell-Permeable Ubiquitin Probe for Temporal Profiling of Deubiquitinating Enzymes. J Am Chem Soc 2020; 142:19493-19501. [PMID: 33141564 DOI: 10.1021/jacs.9b12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photocaged cell-permeable ubiquitin probe holds promise in profiling the activity of cellular deubiquitinating enzymes (DUBs) with the much needed temporal control. Here we report a new photocaged cell-permeable ubiquitin probe that undergoes photoactivation upon 365 nm UV treatment and enables intracellular deubiquitinating enzyme profiling. We used a semisynthetic approach to generate modular ubiquitin-based probe containing a tetrazole-derived warhead at the C-terminus of ubiquitin and employed a cyclic polyarginine cell-penetrating peptide (cR10) conjugated to the N-terminus of ubiquitin via a disulfide linkage to deliver the probe into live cells. Upon 365 nm UV irradiation, the tetrazole group is converted to a nitrilimine intermediate in situ, which reacts with nearby nucleophilic cysteine residue from the DUB active site. The new photocaged cell-permeable probe showed good reactivity toward purified DUBs, including USP2, UCHL1, and UCHL3, upon photoirradiation. The Ub-tetrazole probe was also assessed in HeLa cell lysate and showed robust labeling only upon photoactivation. We further carried out protein profiling in intact HeLa cells using the new photocaged cell-permeable ubiquitin probe and identified DUBs captured by the probe using label-free quantitative (LFQ) mass spectrometry. Importantly, the photocaged cell-permeable ubiquitin probe captured DUBs specifically in respective G1/S and G2/M phases in synchronized HeLa cells. Moreover, using this probe DUBs were profiled at different time points following the release of HeLa cells from G1/S phase. Our results showed that photocaged cell-permeable probe represents a valuable new tool for achieving a better understanding of the cellular functions of DUBs.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Siqi Shen
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
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4
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Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X. Proc Natl Acad Sci U S A 2019; 116:7288-7297. [PMID: 30914461 PMCID: PMC6462090 DOI: 10.1073/pnas.1815027116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ubiquitination is an important posttranslational modification that regulates almost every aspect of cellular functions. Ubiquitin can form chains of different topology; each has a distinctive role in dictating the function and fate of the modified proteins. Deubiquitinases (DUBs) reverse ubiquitination. How DUBs recognize ubiquitin chains is a topic of immense interest due to the therapeutic potentials of human DUBs. We obtained the atomic details of the USP9X catalytic core, a DUB involved in cancers and developmental disorders, and revealed its unusual mechanisms of action using a set of activity-based ubiquitin probes. These probes will propel future investigation of how DUBs recognize and process ubiquitin chains and identify potential new sites on DUBs for drug discovery. USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalytic domain harbors three Ub binding sites, and a zinc finger in the fingers subdomain and the β-hairpin insertion both play important roles in polyUb chain processing and linkage specificity. Furthermore, unexpected labeling of a secondary, noncatalytic cysteine located on a blocking loop adjacent to the catalytic site by K11-diUb ABP implicates a previously unreported mechanism of polyUb chain recognition. The structural features of USP9X revealed in our study are critical for understanding its DUB activity. The new Ub-based ABPs form a set of valuable tools to understand polyUb chain processing by the cysteine protease class of DUBs.
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Masuda Y, Kanao R, Kawai H, Kukimoto I, Masutani C. Preferential digestion of PCNA-ubiquitin and p53-ubiquitin linkages by USP7 to remove polyubiquitin chains from substrates. J Biol Chem 2019; 294:4177-4187. [PMID: 30647135 PMCID: PMC6422070 DOI: 10.1074/jbc.ra118.005167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/22/2018] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) regulates various cellular pathways through its deubiquitination activity. Despite the identification of a growing number of substrates of USP7, the molecular mechanism by which USP7 removes ubiquitin chains from polyubiquitinated substrates remains unexplored. The present study investigated the mechanism underlying the deubiquitination of Lys63-linked polyubiquitinated proliferating cell nuclear antigen (PCNA). Biochemical analyses demonstrated that USP7 efficiently removes polyubiquitin chains from polyubiquitinated PCNA by preferential cleavage of the PCNA-ubiquitin linkage. This property was largely attributed to the poor activity toward Lys63-linked ubiquitin chains. The preferential cleavage of substrate-ubiquitin linkages was also observed for Lys48-linked polyubiquitinated p53 because of the inefficient cleavage of the Lys48-linked ubiquitin chains. The present findings suggest a mechanism underlying the removal of polyubiquitin signals by USP7.
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Affiliation(s)
- Yuji Masuda
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, .,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Rie Kanao
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hidehiko Kawai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan, and
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Chikahide Masutani
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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Kim J, Alavi Naini F, Sun Y, Ma L. Ubiquitin-specific peptidase 2a (USP2a) deubiquitinates and stabilizes β-catenin. Am J Cancer Res 2018; 8:1823-1836. [PMID: 30323974 PMCID: PMC6176183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023] Open
Abstract
β-catenin is not only a key component of adherens junctions but also a transcriptional co-activator downstream of canonical Wnt signaling. The Wnt/β-catenin pathway plays critical roles in animal development and tissue homeostasis, while mutation or overexpression of β-catenin often leads to tumorigenesis and metastasis. Ubiquitination-mediated proteasomal degradation of β-catenin is a key molecular event in the Wnt/β-catenin pathway. Because deubiquitination of β-catenin can stabilize β-catenin and activate Wnt/β-catenin signaling, targeting the β-catenin deubiquitinase may provide a strategy for treating β-catenin-driven cancers. Here, by screening a human deubiquitinase library, we identified USP2a as a deubiquitinase that binds, deubiquitinates, and stabilizes β-catenin protein. USP2a promotes the nuclear accumulation and transcriptional activity of β-catenin, leading to elevated expression of Wnt/β-catenin target genes. Importantly, either genetic knockdown or pharmacological inhibition of USP2a leads to β-catenin destabilization. These findings suggest that USP2a may serve as a therapeutic target for targeting the cancer-promoting protein β-catenin.
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Affiliation(s)
- Jongchan Kim
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Fatemeh Alavi Naini
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Houston Baptist UniversityHouston, Texas 77074, USA
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical SciencesHouston, Texas 77030, USA
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HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome. J Virol 2018; 92:JVI.00037-18. [PMID: 29643240 PMCID: PMC6002723 DOI: 10.1128/jvi.00037-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/02/2018] [Indexed: 11/20/2022] Open
Abstract
HIV protease is known to cause cell death, which is dependent upon cleavage of procaspase 8. HIV protease cleavage of procaspase 8 generates Casp8p41, which directly binds Bak with nanomolar affinity, causing Bak activation and consequent cell death. Casp8p41 can also bind Bcl2 with nanomolar affinity, in which case cell death is averted. Central memory CD4 T cells express high levels of Bcl2, possibly explaining why those cells do not die when they reactivate HIV. Here, we determine that the Casp8p41-Bcl2 complex is polyubiquitinated and degraded by the proteasome. Ixazomib, a proteasome inhibitor in clinical use, blocks this pathway, increasing the abundance of Casp8p41 and causing more cells to die in a Casp8p41-dependent manner. IMPORTANCE The Casp8p41 pathway of cell death is unique to HIV-infected cells yet is blocked by Bcl2. Once bound by Bcl2, Casp8p41 is polyubiquitinated and degraded by the proteasome. Proteasome inhibition blocks degradation of Casp8p41, increasing Casp8p41 levels and causing more HIV-infected cells to die.
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Wu J, Kumar S, Wang F, Wang H, Chen L, Arsenault P, Mattern M, Weinstock J. Chemical Approaches to Intervening in Ubiquitin Specific Protease 7 (USP7) Function for Oncology and Immune Oncology Therapies. J Med Chem 2017; 61:422-443. [DOI: 10.1021/acs.jmedchem.7b00498] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jian Wu
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Suresh Kumar
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Feng Wang
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Hui Wang
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Lijia Chen
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Patrick Arsenault
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Michael Mattern
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Joseph Weinstock
- Progenra, Inc., 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
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9
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Hjortland NM, Mesecar AD. Steady-state kinetic studies reveal that the anti-cancer target Ubiquitin-Specific Protease 17 (USP17) is a highly efficient deubiquitinating enzyme. Arch Biochem Biophys 2016; 612:35-45. [PMID: 27756680 DOI: 10.1016/j.abb.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 12/26/2022]
Abstract
USP17 is a deubiquitinating enzyme that is upregulated in numerous cancers and therefore a drug target. We developed a robust expression, purification, and assay system for USP17 enabling its enzymatic and structural characterization. USP17 was expressed in E. coli as inclusion bodies and then solubilized, refolded, and purified using affinity and size-exclusion chromatography. Milligram quantities of pure USP17 can be produced that is catalytically more efficient (kcat/Km = 1500 (x103) M-1sec-1) than other human USPs studied to date. Analytical size-exclusion chromatography, analytical ultracentrifugation, and dynamic light scattering studies suggest that the quaternary structure of USP17 is a monomer. Steady-state kinetic studies show that USP17 efficiently hydrolyzes both ubiquitin-AMC (kcat = 1.5 sec-1 and Km = 1.0 μM) and ubiquitin-rhodamine110 (kcat = 1.8 sec-1 and Km = 2.0 μM) substrates. Ubiquitin chain cleavage assays reveal that USP17 efficiently cleaves di-ubiquitin chains with Lys11, Lys33, Lys48 and Lys63 linkages and tetra-ubiquitin chains with Lys11, Lys48 and Lys63 linkages but is inefficient in cleaving di-ubiquitin chains with Lys6, Lys27, or Lys29 linkages or linear ubiquitin chains. The substrate specificity of USP17 is most similar to that of USP1, where both USPs display higher specificity than other characterized members of the USP family.
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Affiliation(s)
- Nicole M Hjortland
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, United States
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, United States; Department of Biochemistry, Purdue University, West Lafayette, IN 47906, United States; Department of Chemistry, Purdue University, West Lafayette, IN 47906, United States; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47906, United States.
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Davis MI, Pragani R, Fox JT, Shen M, Parmar K, Gaudiano EF, Liu L, Tanega C, McGee L, Hall MD, McKnight C, Shinn P, Nelson H, Chattopadhyay D, D'Andrea AD, Auld DS, DeLucas LJ, Li Z, Boxer MB, Simeonov A. Small Molecule Inhibition of the Ubiquitin-specific Protease USP2 Accelerates cyclin D1 Degradation and Leads to Cell Cycle Arrest in Colorectal Cancer and Mantle Cell Lymphoma Models. J Biol Chem 2016; 291:24628-24640. [PMID: 27681596 DOI: 10.1074/jbc.m116.738567] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/04/2016] [Indexed: 12/11/2022] Open
Abstract
Deubiquitinases are important components of the protein degradation regulatory network. We report the discovery of ML364, a small molecule inhibitor of the deubiquitinase USP2 and its use to interrogate the biology of USP2 and its putative substrate cyclin D1. ML364 has an IC50 of 1.1 μm in a biochemical assay using an internally quenched fluorescent di-ubiquitin substrate. Direct binding of ML364 to USP2 was demonstrated using microscale thermophoresis. ML364 induced an increase in cellular cyclin D1 degradation and caused cell cycle arrest as shown in Western blottings and flow cytometry assays utilizing both Mino and HCT116 cancer cell lines. ML364, and not the inactive analog 2, was antiproliferative in cancer cell lines. Consistent with the role of cyclin D1 in DNA damage response, ML364 also caused a decrease in homologous recombination-mediated DNA repair. These effects by a small molecule inhibitor support a key role for USP2 as a regulator of cell cycle, DNA repair, and tumor cell growth.
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Affiliation(s)
- Mindy I Davis
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Rajan Pragani
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Jennifer T Fox
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Min Shen
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Kalindi Parmar
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Emily F Gaudiano
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Li Liu
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Cordelle Tanega
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Lauren McGee
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew D Hall
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Crystal McKnight
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Paul Shinn
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Henrike Nelson
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Debasish Chattopadhyay
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alan D D'Andrea
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Douglas S Auld
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Larry J DeLucas
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhuyin Li
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew B Boxer
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
| | - Anton Simeonov
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
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11
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Tencer AH, Liang Q, Zhuang Z. Divergence in Ubiquitin Interaction and Catalysis among the Ubiquitin-Specific Protease Family Deubiquitinating Enzymes. Biochemistry 2016; 55:4708-19. [PMID: 27501351 DOI: 10.1021/acs.biochem.6b00033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Deubiquitinating enzymes (DUBs) are responsible for reversing mono- and polyubiquitination of proteins and play essential roles in numerous cellular processes. Close to 100 human DUBs have been identified and are classified into five families, with the ubiquitin-specific protease (USP) family being the largest (>50 members). The binding of ubiquitin (Ub) to USP is strikingly different from that observed for the DUBs in the ubiquitin C-terminal hydrolase (UCH) and ovarian tumor domain protease (OTU) families. We generated a panel of mutant ubiquitins and used them to probe the ubiquitin's interaction with a number of USPs. Our results revealed a remarkable divergence of USP-Ub interactions among the USP catalytic domains. Our double-mutant cycle analysis targeting the ubiquitin residues located in the tip, the central body, and the tail of ubiquitin also demonstrated different crosstalk among the USP-Ub interactions. This work uncovered intriguing divergence in the ubiquitin-binding mode in the USP family DUBs and raised the possibility of targeting the ubiquitin-binding hot spots on USPs for selective inhibition of USPs by small molecule antagonists.
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Affiliation(s)
- Adam H Tencer
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Qin Liang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
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12
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Affiliation(s)
- Suman Kumar Maity
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
| | - Shimrit Ohayon
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
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13
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Cunningham CN, Baughman JM, Phu L, Tea JS, Yu C, Coons M, Kirkpatrick DS, Bingol B, Corn JE. USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria. Nat Cell Biol 2015; 17:160-9. [PMID: 25621951 DOI: 10.1038/ncb3097] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 12/17/2014] [Indexed: 12/30/2022]
Abstract
Multiple lines of evidence indicate that mitochondrial dysfunction is central to Parkinson's disease. Here we investigate the mechanism by which parkin, an E3 ubiquitin ligase, and USP30, a mitochondrion-localized deubiquitylase, regulate mitophagy. We find that mitochondrial damage stimulates parkin to assemble Lys 6, Lys 11 and Lys 63 chains on mitochondria, and that USP30 is a ubiquitin-specific deubiquitylase with a strong preference for cleaving Lys 6- and Lys 11-linked multimers. Using mass spectrometry, we show that recombinant USP30 preferentially removes these linkage types from intact ubiquitylated mitochondria and counteracts parkin-mediated ubiquitin chain formation in cells. These results, combined with a series of chimaera and localization studies, afford insights into the mechanism by which a balance of ubiquitylation and deubiquitylation regulates mitochondrial homeostasis, and suggest a general mechanism for organelle autophagy.
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Affiliation(s)
- Christian N Cunningham
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Joshua M Baughman
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Lilian Phu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Joy S Tea
- Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Christine Yu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Mary Coons
- Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Baris Bingol
- Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Jacob E Corn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
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14
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Ohayon S, Refua M, Hendler A, Aharoni A, Brik A. Harnessing the Oxidation Susceptibility of Deubiquitinases for Inhibition with Small Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ohayon S, Refua M, Hendler A, Aharoni A, Brik A. Harnessing the oxidation susceptibility of deubiquitinases for inhibition with small molecules. Angew Chem Int Ed Engl 2014; 54:599-603. [PMID: 25327786 DOI: 10.1002/anie.201408411] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 01/08/2023]
Abstract
Deubiquitinases (DUBs) counteract ubiquitination by removing or trimming ubiquitin chains to alter the signal. Their diverse role in biological processes and involvement in diseases have recently attracted great interest with regard to their mechanism and inhibition. It has been shown that some DUBs are regulated by reactive oxygen species (ROS) in which the catalytic Cys residue undergoes reversible oxidation, hence modulating DUBs activity under oxidative stress. Reported herein for the first time, the observation that small molecules, which are capable of generating ROS efficiently, inhibit DUBs by selective and nonreversible oxidation of the catalytic Cys residue. Interestingly, the small molecule beta-lapachone, which is currently in clinical trials for cancer, is among the potent inhibitors, thus suggesting possible new cellular targets for its therapeutic effects. Our study describes a novel mechanism of DUBs inhibition and opens new opportunities in exploiting them for cancer therapy.
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Affiliation(s)
- Shimrit Ohayon
- Department of Chemistry, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501 (Israel)
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Clague MJ, Barsukov I, Coulson JM, Liu H, Rigden DJ, Urbé S. Deubiquitylases from genes to organism. Physiol Rev 2013; 93:1289-315. [PMID: 23899565 DOI: 10.1152/physrev.00002.2013] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ubiquitylation is a major posttranslational modification that controls most complex aspects of cell physiology. It is reversed through the action of a large family of deubiquitylating enzymes (DUBs) that are emerging as attractive therapeutic targets for a number of disease conditions. Here, we provide a comprehensive analysis of the complement of human DUBs, indicating structural motifs, typical cellular copy numbers, and tissue expression profiles. We discuss the means by which specificity is achieved and how DUB activity may be regulated. Generically DUB catalytic activity may be used to 1) maintain free ubiquitin levels, 2) rescue proteins from ubiquitin-mediated degradation, and 3) control the dynamics of ubiquitin-mediated signaling events. Functional roles of individual DUBs from each of five subfamilies in specific cellular processes are highlighted with an emphasis on those linked to pathological conditions where the association is supported by whole organism models. We then specifically consider the role of DUBs associated with protein degradative machineries and the influence of specific DUBs upon expression of receptors and channels at the plasma membrane.
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Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, and Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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Literature Search and Review. Assay Drug Dev Technol 2013. [DOI: 10.1089/adt.2013.1102.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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