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Armstrong LA, Lange SM, Cesare VD, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. Correction: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One 2024; 19:e0302418. [PMID: 38626090 PMCID: PMC11020524 DOI: 10.1371/journal.pone.0302418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0253364.].
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Abdul Rehman SA, Cazzaniga C, Di Nisio E, Antico O, Knebel A, Johnson C, Şahin AT, Ibrahim PEGF, Lamoliatte F, Negri R, Muqit MMK, De Cesare V. Discovery and characterization of noncanonical E2-conjugating enzymes. Sci Adv 2024; 10:eadh0123. [PMID: 38536929 PMCID: PMC10971424 DOI: 10.1126/sciadv.adh0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
E2-conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation, is required to maintain cellular homeostasis and affects almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a posttranslational modification that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry to identify and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We used structural modeling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results unveil the missing E2s necessary for noncanonical ubiquitylation, underscoring the adaptability and versatility of ubiquitin modifications.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Chiara Cazzaniga
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Elena Di Nisio
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Clare Johnson
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alp T Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow St, Dundee DD1 5EH, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Rome, Italy
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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Traynor R, Moran J, Stevens M, Antico O, Knebel A, Behrouz B, Merchant K, Hastie CJ, Davies P, Muqit MMK, De Cesare V. Design and high-throughput implementation of MALDI-TOF/MS-based assays for Parkin E3 ligase activity. Cell Rep Methods 2024; 4:100712. [PMID: 38382522 PMCID: PMC10921019 DOI: 10.1016/j.crmeth.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Parkinson's disease (PD) is a progressive neurological disorder that manifests clinically as alterations in movement as well as multiple non-motor symptoms including but not limited to cognitive and autonomic abnormalities. Loss-of-function mutations in the gene encoding the ubiquitin E3 ligase Parkin are causal for familial and juvenile PD. Among several therapeutic approaches being explored to treat or improve the prognosis of patients with PD, the use of small molecules able to reinstate or boost Parkin activity represents a potential pharmacological treatment strategy. A major barrier is the lack of high-throughput platforms for the robust and accurate quantification of Parkin activity in vitro. Here, we present two different and complementary Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF/MS)-based approaches for the quantification of Parkin E3 ligase activity in vitro. Both approaches are scalable for high-throughput primary screening to facilitate the identification of Parkin modulators.
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Affiliation(s)
- Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Bahareh Behrouz
- Vincere Biosciences, Inc., 245 Main St. Fl 2, Cambridge, MA 02142, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, School of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK.
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De Cesare V. MALDI-TOF Mass Spectrometry for interrogating ubiquitin enzymes. Front Mol Biosci 2023; 10:1184934. [PMID: 37234921 PMCID: PMC10206504 DOI: 10.3389/fmolb.2023.1184934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
The attachment of ubiquitin to a substrate (ubiquitination or ubiquitylation) impacts its lifetime and regulates its function within the cell. Several classes of enzymes oversee the attachment of ubiquitin to the substrate: an E1 activating enzyme that makes ubiquitin chemically susceptible prior to the following stages of conjugation and ligation, respectively mediated by E2 conjugating enzymes (E2s) and E3 ligases (E3s). Around 40 E2s and more than 600 E3s are encoded in the human genome, and their combinatorial and cooperative behaviour dictate the tight specificity necessary for the regulation of thousands of substrates. The removal of ubiquitin is orchestrated by a network of about 100 deubiquitylating enzymes (DUBs). Many cellular processes are tightly controlled by ubiquitylation, which is essential in maintaining cellular homeostasis. Because of the fundamental role(s) of ubiquitylation, there is an interest in better understanding the function and specificity of the ubiquitin machinery. Since 2014, an expanding array of Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) Mass Spectrometry (MS) assays have been developed to systematically characterise the activity of a variety of ubiquitin enzymes in vitro. Here we recapitulate how MALDI-TOF MS aided the in vitro characterization of ubiquitin enzymes and the discovery of new and unexpected of E2s and DUBs functions. Given the versatility of the MALDI-TOF MS approach, we foreseen the use of this technology to further expand our understanding of ubiquitin and ubiquitin-like enzymes.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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De Cesare V, Davies P. High-Throughput MALDI-TOF Mass Spectrometry-Based Deubiquitylating Enzyme Assay for Drug Discovery. Methods Mol Biol 2023; 2591:123-134. [PMID: 36350546 DOI: 10.1007/978-1-0716-2803-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ubiquitylation (or ubiquitination) is the reversible conjugation of a 76-amino-acid polypeptide (ubiquitin) to a target protein to modulate various biological processes. Deubiquitylating enzymes (DUBs) are a class of enzymes that specifically remove ubiquitin from a substrate. In recent years DUBs have garnered significant attention as a new class of targets in multiple therapeutic areas. The recent development of high-throughput Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS) has provided new tools to perform drug discovery screening. Here we present a facile and high-throughput step-by-step protocol of the MALDI-TOF MS-based DUB assay for screening the activity of DUBs in vitro. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains. The presented protocol takes advantage of nanoliter dispensing robotics and automated MALDI-TOF MS analysis to screen large and diverse compound libraries.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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Haag A, Rapun-Araiz B, Cesare VD, Dorado-Morales P, Penadés J, Lasa I. Systematic Reconstruction of the Complete Two-Component Sensorial Network in Staphylococcus aureus. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, adaptation to changes in the environment is mainly controlled through two-component signal transduction systems (TCSs). Most bacteria contain dozens of TCSs, each of them responsible for sensing a different range of signals and controlling the expression of a repertoire of target genes (regulon). Frequently, TCS control key physiological changes required for pathogenesis and/or antimicrobial resistance. Over the years, identification of the regulon controlled by each individual TCS in different bacteria has been a recurrent question. However, limitations associated with the classical approaches used have left our knowledge far from complete. In this report, using a pioneering approach in which a strain devoid of the complete nonessential TCS network was systematically complemented with the constitutively active form of each response regulator, we have reconstituted the regulon of each TCS of S. aureus in the absence of interference between members of the family. Transcriptome sequencing (RNA-Seq) and proteomics allowed us to determine the size, complexity, and insulation of each regulon and to identify the genes regulated exclusively by one or many TCSs. This gain-of-function strategy provides the first description of the complete TCS regulon in a living cell, which we expect will be useful to understand the pathobiology of this important pathogen.
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Affiliation(s)
- Andreas Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom
| | - Beatriz Rapun-Araiz
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Spain
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom
| | - Pedro Dorado-Morales
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Spain
| | - José Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, Spain
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Spain
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De Cesare V, Moran J, Traynor R, Knebel A, Ritorto MS, Trost M, McLauchlan H, Hastie CJ, Davies P. High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry-based deubiquitylating enzyme assay for drug discovery. Nat Protoc 2020; 15:4034-4057. [PMID: 33139956 DOI: 10.1038/s41596-020-00405-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF-based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry-based readout.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.,Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
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De Cesare V, Johnson C, Barlow V, Hastie J, Knebel A, Trost M. The MALDI-TOF E2/E3 Ligase Assay as Universal Tool for Drug Discovery in the Ubiquitin Pathway. Cell Chem Biol 2018; 25:1117-1127.e4. [PMID: 30017913 PMCID: PMC6162346 DOI: 10.1016/j.chembiol.2018.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/14/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
Due to their role in many diseases, enzymes of the ubiquitin system have recently become interesting drug targets. Despite efforts, primary screenings of compound libraries targeting E2 enzymes and E3 ligases have been strongly limited by the lack of robust and fast high-throughput assays. Here we report a label-free high-throughput screening assay for ubiquitin E2 conjugating enzymes and E3 ligases based on MALDI-TOF mass spectrometry. The MALDI-TOF E2/E3 assay allows testing E2 enzymes and E3 ligases for their ubiquitin transfer activity, identifying E2/E3 active pairs, inhibitor potency and specificity and screening compound libraries in vitro without chemical or fluorescent probes. We demonstrate that the MALDI-TOF E2/E3 assay is a universal tool for drug discovery screening in the ubiquitin pathway as it is suitable for working with all E3 ligase families and requires a reduced amount of reagents, compared with standard biochemical assays. We have developed a high-throughput MALDI-TOF assay for E2/E3 enzymes It allows screening compound libraries without chemical or fluorescent probes We tested the screen on three disease-relevant E3 ligases: MDM2, ITCH, and HOIP We performed a proof-of-concept high-throughput screen against 1,430 compounds
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK.
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Victoria Barlow
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 1HH, UK.
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Kwasna D, Abdul Rehman SA, Natarajan J, Matthews S, Madden R, De Cesare V, Weidlich S, Virdee S, Ahel I, Gibbs-Seymour I, Kulathu Y. Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability. Mol Cell 2018; 70:150-164.e6. [PMID: 29576527 PMCID: PMC5896202 DOI: 10.1016/j.molcel.2018.02.023] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.
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Affiliation(s)
- Dominika Kwasna
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jayaprakash Natarajan
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen Matthews
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ross Madden
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ivan Ahel
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Ian Gibbs-Seymour
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Magiera K, Tomala M, Kubica K, De Cesare V, Trost M, Zieba BJ, Kachamakova-Trojanowska N, Les M, Dubin G, Holak TA, Skalniak L. Lithocholic Acid Hydroxyamide Destabilizes Cyclin D1 and Induces G 0/G 1 Arrest by Inhibiting Deubiquitinase USP2a. Cell Chem Biol 2017; 24:458-470.e18. [PMID: 28343940 PMCID: PMC5404848 DOI: 10.1016/j.chembiol.2017.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 09/26/2016] [Accepted: 03/01/2017] [Indexed: 12/29/2022]
Abstract
USP2a is a deubiquitinase responsible for stabilization of cyclin D1, a crucial regulator of cell-cycle progression and a proto-oncoprotein overexpressed in numerous cancer types. Here we report that lithocholic acid (LCA) derivatives are inhibitors of USP proteins, including USP2a. The most potent LCA derivative, LCA hydroxyamide (LCAHA), inhibits USP2a, leading to a significant Akt/GSK3β-independent destabilization of cyclin D1, but does not change the expression of p27. This leads to the defects in cell-cycle progression. As a result, LCAHA inhibits the growth of cyclin D1-expressing, but not cyclin D1-negative cells, independently of the p53 status. We show that LCA derivatives may be considered as future therapeutics for the treatment of cyclin D1-addicted p53-expressing and p53-defective cancer types.
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Affiliation(s)
- Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Marcin Tomala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bartosz J Zieba
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Neli Kachamakova-Trojanowska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Marcin Les
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
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11
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Licursi V, Salvi C, De Cesare V, Rinaldi T, Mattei B, Fabbri C, Serino G, Bramasole L, Zimbler JZ, Pick E, Barnes BM, Bard M, Negri R. The COP9 signalosome is involved in the regulation of lipid metabolism and of transition metals uptake inSaccharomyces cerevisiae. FEBS J 2013; 281:175-90. [DOI: 10.1111/febs.12584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/12/2013] [Accepted: 10/08/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Valerio Licursi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Chiara Salvi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Virginia De Cesare
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Teresa Rinaldi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Benedetta Mattei
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Claudia Fabbri
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Giovanna Serino
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Laylan Bramasole
- Department of Biology; University of Haifa at Oranim; Tivon Israel
| | - Jacob Z. Zimbler
- Department of Biology; University of Haifa at Oranim; Tivon Israel
- Department of Evolutionary and Environmental Biology; University of Haifa; Israel
| | - Elah Pick
- Department of Biology; University of Haifa at Oranim; Tivon Israel
- Department of Evolutionary and Environmental Biology; University of Haifa; Israel
| | - Brett M. Barnes
- Department of Biology; Indiana University - Purdue University; Indianapolis IN USA
| | - Martin Bard
- Department of Biology; Indiana University - Purdue University; Indianapolis IN USA
| | - Rodolfo Negri
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
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