1
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Chen J, Wang Y, Wang R, Yuan R, Chu GC, Li YM. Chemical synthesis of on demand-activated SUMO-based probe by a photocaged glycine-assisted strategy. Bioorg Med Chem Lett 2023; 94:129460. [PMID: 37640164 DOI: 10.1016/j.bmcl.2023.129460] [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: 07/11/2023] [Revised: 08/05/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
The transiently-activated SUMO probes are conducive to understand the dynamic control of SENPs activity. Here, we developed a photocaged glycine-assisted strategy for the construction of on demand-activated SUMO-ABPs. The light-sensitive groups installed at G92 and G64 backbone of SUMO-2 can temporarily block probes activity and hamper aspartimide formation, respectively, which enabled the efficient synthesis of inert SUMO-2 propargylamide (PA). The probe could be activated to capture SENPs upon photo-irradiation not only in vitro but also in intact cells, providing opportunities to further perform intracellular time-resolved proteome-wide profiling of SUMO-related enzymes.
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Affiliation(s)
- Jingnan Chen
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Yu Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
| | - Rongtian Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Rujing Yuan
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Guo-Chao Chu
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
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2
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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3
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Qin Y, Zhang X, Song Y, Zhong B, Liu L, Wang D, Zhang Y, Lu W, Zhao X, Jia Z, Li M, Zhang L, Qing G. A highly sensitive nanochannel device for the detection of SUMO1 peptides. Chem Sci 2023; 14:8360-8368. [PMID: 37564410 PMCID: PMC10411628 DOI: 10.1039/d3sc02140h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023] Open
Abstract
SUMOylation is an important and highly dynamic post-translational modification (PTM) process of protein, and its disequilibrium may cause various diseases, such as cancers and neurodegenerative disorders. SUMO proteins must be accurately detected to understand disease states and develop effective drugs. Reliable antibodies against SUMO2/3 are commercially available; however, efficient detectors are yet to be developed for SUMO1, which has only 50% homology with SUMO2 and SUMO3. Here, using phage display technology, we identified two cyclic peptide (CP) sequences that could specifically bind to the terminal dodecapeptide sequence of SUMO1. Then we combined the CPs and polyethylene terephthalate conical nanochannel films to fabricate a nanochannel device highly sensitive towards the SUMO1 terminal peptide and protein; sensitivity was achieved by ensuring marked variations in both transmembrane ionic current and Faraday current. The satisfactory SUMO1-sensing ability of this device makes it a promising tool for the time-point monitoring of the SENP1 enzyme-catalyzed de-SUMOylation reaction and cellular imaging. This study not only solves the challenge of SUMO1 precise recognition that could promote SUMO1 proteomics analysis, but also demonstrates the good potential of the nanochannel device in monitoring of enzymes and discovery of effective drugs.
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Affiliation(s)
- Yue Qin
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Xiaoyu Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Yanling Song
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Lu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Dongdong Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Yahui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Wenqi Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Zhiqi Jia
- College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology No. 11 Street, Economic and Technological Development Zone Shenyang 110142 P. R. China
| | - Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
- College of Chemistry and Chemical Engineering, Wuhan Textile University 1 Sunshine Road Wuhan 430200 P. R. China
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4
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Total Chemical Synthesis of LC3A and LC3B Activity-Based Probes. Biomedicines 2023; 11:biomedicines11030884. [PMID: 36979862 PMCID: PMC10045837 DOI: 10.3390/biomedicines11030884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Autophagy is a conserved cellular process involved in the degradation of intercellular materials. During this process, double-membrane vesicles called autophagosomes engulf cytoplasmic components ready for degradation. A key component in the formation of autophagosomes are the autophagy-related (Atg) proteins, including microtubule-associated protein light chain 3A (LC3A) and 3B (LC3B). After the C-terminus of LC3 is conjugated to a phospholipid, it promotes the elongation of the phagosome and provides a docking station for the delivery of proteins ready for degradation. Since dysregulation of the autophagy pathway has been associated with a variety of human diseases, components of this process have been considered as potential therapeutic targets. However, the mechanistic details of LC3-specific ligases and deconjugation enzymes are far from unraveled and chemical tools for activity profiling could aid in affording more insights into this process. Herein, we describe a native chemical ligation approach for the synthesis of two LC3 activity-based probes (ABPs). Initial studies show that the probes covalently interact with the cysteine protease ATG4B, showcasing the potential of these probes to unravel mechanistic and structural details.
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5
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Shu X, Liao QQ, Li ST, Liu L, Zhang X, Zhou L, Zhang L, Coin I, Wang L, Wu H, Yang B. Detecting Active Deconjugating Enzymes with Genetically Encoded Activity-Based Ubiquitin and Ubiquitin-like Protein Probes. Anal Chem 2023; 95:846-853. [PMID: 36595388 DOI: 10.1021/acs.analchem.2c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Post-translational modification of proteins by Ubiquitin (Ub) and Ubiquitin-like proteins (Ubls) can be reversed by deconjugating enzymes, which have been implicated in different pathways and associated with various human diseases. To understand the activity and dynamics of deconjugating enzymes, multiple synthetic and semi-synthetic Ub/Ubl probes have been developed, and some of them have been applied to screen inhibitors of deconjugating enzymes. Since these Ub/Ubl probes are generally not cell-permeable, different strategies have been developed to deliver Ub/Ubl probes to live cells. However, till now, no Ub/Ubl probes can be expressed in live cells to directly report on the activities of deconjugating enzymes in the most relevant cellular environment. Here, we genetically encoded cross-linkable Ub/Ubl probes in live E. coli and HEK293T cells. These probes can cross-link with deconjugating enzymes in vitro and in vivo. Using these Ub probes combined with mass spectrometry, we have successfully identified endogenous deconjugating enzymes in live cells. We believe that these genetically encoded Ub/Ubl probes are valuable for investigating biological functions of deconjugating enzymes in physiological environments.
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Affiliation(s)
- Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing-Qing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shang-Tong Li
- Glbizzia Biosciences Company Limited, Beijing 102601, China
| | - Lu Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig 04103, Germany
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
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6
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Huppelschoten Y, Buchardt J, Nielsen TE, van der Heden van Noort GJ. Total Linear Chemical Synthesis of LC3A and LC3B. Methods Mol Biol 2023; 2602:51-61. [PMID: 36446966 DOI: 10.1007/978-1-0716-2859-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Solid-phase peptide synthesis (SPPS) enables the synthesis of chemically modified peptides and proteins. Chemically synthesized ubiquitin(-like) proteins containing a fluorescent tag or reactive warhead have proven to be important tools in elucidating biological processes. Here, we describe the first fully synthetic method for the linear synthesis of two LC3 ubiquitin-like proteins using disaggregating building blocks and heated synthesis. Both LC3A and LC3B were synthesized and equipped with a fluorescent rhodamine tag, followed by folding of the proteins and liquid chromatography-mass spectrometry and SDS-PAGE analysis to prove that the quality of the synthetic material is comparable to expressed material.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
- Global Research Technologies, Novo Nordisk, Novo Nordisk Park, Måløv, Denmark
| | - Jens Buchardt
- Global Research Technologies, Novo Nordisk, Novo Nordisk Park, Måløv, Denmark
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7
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Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe. Sci China Chem 2023; 66:837-844. [PMID: 36684644 PMCID: PMC9840423 DOI: 10.1007/s11426-022-1455-x] [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: 09/05/2022] [Accepted: 11/08/2022] [Indexed: 01/15/2023]
Abstract
ISG15 is a ubiquitin-like (Ubl) protein attached to substrate proteins by ISG15 conjugating enzymes whose dysregulation is implicated in a multitude of disease processes, but the probing of these enzymes remains to be accomplished. Here, we describe the development of a new activity-based probe ISG15-Dha (dehydroalanine) through protein semi-synthesis. In vitro cross-linking and cell lysate proteomic profiling experiments showed that this probe can sequentially capture ISG15 conjugating enzymes including E1 enzyme UBA7, E2 enzyme UBE2L6, E3 enzyme HERC5, the previously known ISG15 deconjugating enzyme (USP18), as well as some other enzymes (USP5 and USP14) which we additionally confirmed to impart deISGylation activity. Collectively, ISG15-Dha provides a new tool that can simultaneously capture ISG15 conjugating and deconjugating enzymes for biochemical or pharmacological studies. Electronic Supplementary Material Supplementary material is available for this article at 10.1007/s11426-022-1455-x and is accessible for authorized users.
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8
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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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9
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Huppelschoten Y, van der Heden van Noort GJ. State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools. Semin Cell Dev Biol 2022; 132:74-85. [PMID: 34961664 DOI: 10.1016/j.semcdb.2021.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; Global Research Technologies, Novo Nordisk Research Park, Måløv, Denmark
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10
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022; 61:e202203792. [DOI: 10.1002/anie.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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11
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Vertegaal ACO. Signalling mechanisms and cellular functions of SUMO. Nat Rev Mol Cell Biol 2022; 23:715-731. [PMID: 35750927 DOI: 10.1038/s41580-022-00500-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 12/22/2022]
Abstract
Sumoylation is an essential post-translational modification that is catalysed by a small number of modifying enzymes but regulates thousands of target proteins in a dynamic manner. Small ubiquitin-like modifiers (SUMOs) can be attached to target proteins as one or more monomers or in the form of polymers of different types. Non-covalent readers recognize SUMO-modified proteins via SUMO interaction motifs. SUMO simultaneously modifies groups of functionally related proteins to regulate predominantly nuclear processes, including gene expression, the DNA damage response, RNA processing, cell cycle progression and proteostasis. Recent progress has increased our understanding of the cellular and pathophysiological roles of SUMO modifications, extending their functions to the regulation of immunity, pluripotency and nuclear body assembly in response to oxidative stress, which partly occurs through the recently characterized mechanism of liquid-liquid phase separation. Such progress in understanding the roles and regulation of sumoylation opens new avenues for the targeting of SUMO to treat disease, and indeed the first drug blocking sumoylation is currently under investigation in clinical trials as a possible anticancer agent.
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Affiliation(s)
- Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.
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12
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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13
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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14
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Insights in Post-Translational Modifications: Ubiquitin and SUMO. Int J Mol Sci 2022; 23:ijms23063281. [PMID: 35328702 PMCID: PMC8952880 DOI: 10.3390/ijms23063281] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Both ubiquitination and SUMOylation are dynamic post-translational modifications that regulate thousands of target proteins to control virtually every cellular process. Unfortunately, the detailed mechanisms of how all these cellular processes are regulated by both modifications remain unclear. Target proteins can be modified by one or several moieties, giving rise to polymers of different morphology. The conjugation cascades of both modifications comprise a few activating and conjugating enzymes but close to thousands of ligating enzymes (E3s) in the case of ubiquitination. As a result, these E3s give substrate specificity and can form polymers on a target protein. Polymers can be quickly modified forming branches or cleaving chains leading the target protein to its cellular fate. The recent development of mass spectrometry(MS) -based approaches has increased the understanding of ubiquitination and SUMOylation by finding essential modified targets in particular signaling pathways. Here, we perform a concise overview comprising from the basic mechanisms of both ubiquitination and SUMOylation to recent MS-based approaches aimed to find specific targets for particular E3 enzymes.
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Mann G, Sadhu P, Brik A. Multiplexed Delivery of Synthetic (Un)Conjugatable Ubiquitin and SUMO2 Enables Simultaneous Monitoring of their Localization and Function in Live Cells. Chembiochem 2022; 23:e202200122. [PMID: 35235714 PMCID: PMC9401080 DOI: 10.1002/cbic.202200122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Ubiquitin (Ub) and its related small Ub like modifier (SUMO) are among the most influential protein post‐translational modifications in eukaryotes. Unfortunately, visualizing these modifications in live cells is a challenging task. Chemical protein synthesis offers great opportunities in studying and further understanding Ub and SUMO biology. Nevertheless, the low cell permeability of proteins limits these studies mainly for in vitro applications. Here, we introduce a multiplexed protein cell delivery approach, termed MBL (multiplexed bead loading), for simultaneous loading of up to four differentially labeled proteins with organic fluorophores. We applied MBL to visualize ubiquitination and SUMOylation events in live and untransfected cells without fluorescent protein tags or perturbation to their endogenous levels. Our study reveals unprecedented involvements of Ub and SUMO2 in lysosomes depending on conjugation states. We envision that this approach will improve our understanding of dynamic cellular processes such as formation and disassembly of membraneless organelles.
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Affiliation(s)
- Guy Mann
- Technion Israel Institute of Technology, Schulich faculty of chemistry, ISRAEL
| | - Pradeep Sadhu
- Technion Israel Institute of Technology, Schulich faculty of chemistry, ISRAEL
| | - Ashraf Brik
- Technion-Israel Institue of Technology, Schulich Faculty of chemistry, Technion City, 32000, Haifa, ISRAEL
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16
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Mandal S, Mann G, Satish G, Brik A. Enhanced Live-Cell Delivery of Synthetic Proteins Assisted by Cell-Penetrating Peptides Fused to DABCYL. Angew Chem Int Ed Engl 2021; 60:7333-7343. [PMID: 33615660 PMCID: PMC8048964 DOI: 10.1002/anie.202016208] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Indexed: 12/13/2022]
Abstract
Live-cell delivery of a fully synthetic protein having selectivity towards a particular target is a promising approach with potential applications for basic research and therapeutics. Cell-penetrating peptides (CPPs) allow the cellular delivery of proteins but mostly result in endosomal entrapment, leading to lack of bioavailability. Herein, we report the design and synthesis of a CPP fused to 4-((4-(dimethylamino)phenyl)azo)benzoic acid (DABCYL) to enhance cellular uptake of fluorescently labelled synthetic protein analogues in low micromolar concentration. The attachment of cyclic deca-arginine (cR10) modified with a single lysine linked to DABCYL to synthetic ubiquitin (Ub) and small ubiquitin-like modifier-2 (SUMO-2) scaffolds resulted in a threefold higher uptake efficacy in live cells compared to the unmodified cR10. We could also achieve cR10DABCYL-assisted delivery of Ub and a Ub variant (Ubv) based activity-based probes for functional studies of deubiquitinases in live cells.
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Affiliation(s)
- Shaswati Mandal
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology3200008HaifaIsrael
| | - Guy Mann
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology3200008HaifaIsrael
| | - Gandhesiri Satish
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology3200008HaifaIsrael
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology3200008HaifaIsrael
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17
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Mandal S, Mann G, Satish G, Brik A. Enhanced Live‐Cell Delivery of Synthetic Proteins Assisted by Cell‐Penetrating Peptides Fused to DABCYL. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shaswati Mandal
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology 3200008 Haifa Israel
| | - Guy Mann
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology 3200008 Haifa Israel
| | - Gandhesiri Satish
- 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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18
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Sarkar D, Harms H, Galleano I, Sheikh ZP, Pless SA. Ion channel engineering using protein trans-splicing. Methods Enzymol 2021; 654:19-48. [PMID: 34120713 DOI: 10.1016/bs.mie.2021.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Conventional site-directed mutagenesis and genetic code expansion approaches have been instrumental in providing detailed functional and pharmacological insight into membrane proteins such as ion channels. Recently, this has increasingly been complemented by semi-synthetic strategies, in which part of the protein is generated synthetically. This means a vast range of chemical modifications, including non-canonical amino acids (ncAA), backbone modifications, chemical handles, fluorescent or spectroscopic labels and any combination of these can be incorporated. Among these approaches, protein trans-splicing (PTS) is particularly promising for protein reconstitution in live cells. It relies on one or more split inteins, which can spontaneously and covalently link flanking peptide or protein sequences. Here, we describe the use of PTS and its variant tandem PTS (tPTS) in semi-synthesis of ion channels in Xenopus laevis oocytes to incorporate ncAAs, post-translational modifications or metabolically stable mimics thereof. This strategy has the potential to expand the type and number of modifications in ion channel research.
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Affiliation(s)
- Debayan Sarkar
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hendrik Harms
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Zeshan Pervez Sheikh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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19
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Abboud SA, Cisse EH, Doudeau M, Bénédetti H, Aucagne V. A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation. Chem Sci 2021; 12:3194-3201. [PMID: 34164087 PMCID: PMC8179351 DOI: 10.1039/d0sc06001a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - El Hadji Cisse
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
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20
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Mulder MPC, Kessler BM. In Memoriam: Professor Huib Ovaa (1973-2020): A Uniquely Brilliant and Enthusiastic Scientist, a Pioneer in Chemical Biology and the Ubiquitin Field. Front Chem 2020. [PMCID: PMC7468445 DOI: 10.3389/fchem.2020.00627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Monique P. C. Mulder
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
- *Correspondence: Monique P. C. Mulder
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Benedikt M. Kessler
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21
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Sui X, Wang Y, Du YX, Liang LJ, Zheng Q, Li YM, Liu L. Development and application of ubiquitin-based chemical probes. Chem Sci 2020; 11:12633-12646. [PMID: 34123237 PMCID: PMC8163311 DOI: 10.1039/d0sc03295f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein ubiquitination regulates almost every process in eukaryotic cells. The study of the many enzymes involved in the ubiquitination system and the development of ubiquitination-associated therapeutics are important areas of current research. Synthetic tools such as ubiquitin-based chemical probes have been making an increasing contribution to deciphering various biochemical components involved in ubiquitin conjugation, recruitment, signaling, and deconjugation. In the present minireview, we summarize the progress of ubiquitin-based chemical probes with an emphasis on their various structures and chemical synthesis. We discuss the utility of the ubiquitin-based chemical probes for discovering and profiling ubiquitin-dependent signaling systems, as well as the monitoring and visualization of ubiquitin-related enzymatic machinery. We also show how the probes can serve to elucidate the molecular mechanism of recognition and catalysis. Collectively, the development and application of ubiquitin-based chemical probes emphasizes the importance and utility of chemical protein synthesis in modern chemical biology. This article reviews the design, synthesis, and application of different classes of Ub-based chemical probes.![]()
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China .,Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yu Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Yun-Xiang Du
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
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22
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Hassan MM, Olaoye OO. Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors. Molecules 2020; 25:E2285. [PMID: 32414020 PMCID: PMC7288102 DOI: 10.3390/molecules25102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Olasunkanmi O. Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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23
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Hu H. Recent Advances of Bioresponsive Nano-Sized Contrast Agents for Ultra-High-Field Magnetic Resonance Imaging. Front Chem 2020; 8:203. [PMID: 32266217 PMCID: PMC7100386 DOI: 10.3389/fchem.2020.00203] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
The ultra-high-field magnetic resonance imaging (MRI) nowadays has been receiving enormous attention in both biomaterial research and clinical diagnosis. MRI contrast agents are generally comprising of T1-weighted and T2-weighted contrast agent types, where T1-weighted contrast agents show positive contrast enhancement with brighter images by decreasing the proton's longitudinal relaxation times and T2-weighted contrast agents show negative contrast enhancement with darker images by decreasing the proton's transverse relaxation times. To meet the incredible demand of MRI, ultra-high-field T2 MRI is gradually attracting the attention of research and medical needs owing to its high resolution and high accuracy for detection. It is anticipated that high field MRI contrast agents can achieve high performance in MRI imaging, where parameters of chemical composition, molecular structure and size of varied contrast agents show contrasted influence in each specific diagnostic test. This review firstly presents the recent advances of nanoparticle contrast agents for MRI. Moreover, multimodal molecular imaging with MRI for better monitoring is discussed during biological process. To fasten the process of developing better contrast agents, deep learning of artificial intelligent (AI) can be well-integrated into optimizing the crucial parameters of nanoparticle contrast agents and achieving high resolution MRI prior to the clinical applications. Finally, prospects and challenges are summarized.
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Affiliation(s)
- Hailong Hu
- School of Aeronautics and Astronautics, Central South University, Changsha, China
- Research Center in Intelligent Thermal Structures for Aerospace, Central South University, Changsha, China
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24
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Liebelt F, Sebastian RM, Moore CL, Mulder MPC, Ovaa H, Shoulders MD, Vertegaal ACO. SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat Shock. Cell Rep 2020; 26:236-249.e4. [PMID: 30605679 PMCID: PMC6316133 DOI: 10.1016/j.celrep.2018.12.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/22/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The role of stress-induced increases in SUMO2/3 conjugation during the heat shock response (HSR) has remained enigmatic. We investigated SUMO signal transduction at the proteomic and functional level during the HSR in cells depleted of proteostasis network components via chronic heat shock factor 1 inhibition. In the recovery phase post heat shock, high SUMO2/3 conjugation was prolonged in cells lacking sufficient chaperones. Similar results were obtained upon inhibiting HSP90, indicating that increased chaperone activity during the HSR is critical for recovery to normal SUMO2/3 levels post-heat shock. Proteasome inhibition likewise prolonged SUMO2/3 conjugation, indicating that stress-induced SUMO2/3 targets are subsequently degraded by the ubiquitin-proteasome system. Functionally, we suggest that SUMOylation can enhance the solubility of target proteins upon heat shock, a phenomenon that we experimentally observed in vitro. Collectively, our results implicate SUMO2/3 as a rapid response factor that coordinates proteome degradation and assists the maintenance of proteostasis upon proteotoxic stress. Chaperone depletion delays recovery of SUMOylation in response to heat shock SUMOylated proteins are targeted to the proteasome during heat shock recovery Chaperone depletion impairs clearance of Ub/SUMO co-modified proteins after stress SUMO is a rapid response factor likely increasing protein solubility under heat shock
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Affiliation(s)
- Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monique P C Mulder
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands.
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25
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Pérez Berrocal DA, Witting KF, Ovaa H, Mulder MPC. Hybrid Chains: A Collaboration of Ubiquitin and Ubiquitin-Like Modifiers Introducing Cross-Functionality to the Ubiquitin Code. Front Chem 2020; 7:931. [PMID: 32039151 PMCID: PMC6987259 DOI: 10.3389/fchem.2019.00931] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 01/31/2023] Open
Abstract
The Ubiquitin CODE constitutes a unique post-translational modification language relying on the covalent attachment of Ubiquitin (Ub) to substrates, with Ub serving as the minimum entity to generate a message that is translated into different cellular pathways. The creation of this message is brought about by the dedicated action of writers, erasers, and readers of the Ubiquitin CODE. This CODE is greatly expanded through the generation of polyUb chains of different architectures on substrates thus regulating their fate. Through additional post-translational modification by Ub-like proteins (UbL), hybrid Ub/UbL chains, which either alter the originally encrypted message or encode a completely new one, are formed. Hybrid Ub/UbL chains are generated under both stress or physiological conditions and seem to confer improved specificity and affinity toward their cognate receptors. In such a manner, their formation must play a specific, yet still undefined role in cellular signaling and thus understanding the UbCODE message is crucial. Here, we discuss the evidence for the existence of hybrid Ub/UbL chains in addition to the current understanding of its biology. The modification of Ub by another UbL complicates the deciphering of the spatial and temporal order of events warranting the development of a hybrid chain toolbox. We discuss this unmet need and expand upon the creation of tailored tools adapted from our previously established toolkit for the Ubiquitin Proteasome System to specifically target these hybrid Ub/UbL chains.
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Affiliation(s)
- David A Pérez Berrocal
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Katharina F Witting
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
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26
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Jia Y, Claessens LA, Vertegaal ACO, Ovaa H. Chemical Tools and Biochemical Assays for SUMO Specific Proteases (SENPs). ACS Chem Biol 2019; 14:2389-2395. [PMID: 31361113 PMCID: PMC6862319 DOI: 10.1021/acschembio.9b00402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SUMOylation is a reversible and highly dynamic post-translational modification of target proteins by small ubiquitin-like modifiers (SUMO). It is orchestrated by SUMO-activating, -conjugating, and -ligating enzymes in a sequential manner and is important in regulating a myriad of predominantly nuclear processes. DeSUMOylation is achieved by SUMO-specific proteases (SENPs). Deregulation of SUMOylation and deSUMOylation results in cellular dysfunction and is linked to various diseases, including cancer. In recent years, SENPs have emerged as potential therapeutic targets. In this review, we will describe the inhibitors and activity-based probes of SENPs. Furthermore, we will summarize the biochemical assays available for evaluating the activity of SENPs to identify inhibitors.
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Affiliation(s)
- Yuqing Jia
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura A. Claessens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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27
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Fan J, Ye Y, Chu G, Zhang Z, Fu Y, Li YM, Shi J. Semisynthesis of Ubiquitin and SUMO-Rhodamine 110-Glycine through Aminolysis of Boc-Protected Thioester Counterparts. J Org Chem 2019; 84:14861-14867. [PMID: 31642325 DOI: 10.1021/acs.joc.9b01529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-based fluorescent reagents are crucial to explore the activity of deubiquitinases (DUBs). Ub-Rho110-G is one of the preferred tools, whereas the current synthetic route is time-consuming. Here, we report a new semisynthetic strategy to produce Ub-Rho110-G through direct aminolysis of Boc-protected Ub-Mesna using bisglycyl-rhodamine 110. We also applied this strategy to synthesize active SUMO2-Rho110-G for the first time. Biochemical analysis demonstrated that semisynthetic Ub or SUMO-Rho110-G can be effectively used for the detection of the activity of DUBs or SUMO-specific enzymes.
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Affiliation(s)
- Jian Fan
- Department of Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Yinshan Ye
- School of Food and Biological Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China
| | - Guochao Chu
- Department of Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Zhongping Zhang
- Institute of Intelligent Machines , Chinese Academy of Sciences , Hefei , Anhui 230031 , China
| | - Yao Fu
- Department of Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Yi-Ming Li
- School of Food and Biological Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China
| | - Jing Shi
- Department of Chemistry , University of Science and Technology of China , Hefei 230026 , China
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28
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Bouchenna J, Sénéchal M, Drobecq H, Stankovic-Valentin N, Vicogne J, Melnyk O. The Role of the Conserved SUMO-2/3 Cysteine Residue on Domain Structure Investigated Using Protein Chemical Synthesis. Bioconjug Chem 2019; 30:2684-2696. [PMID: 31532181 DOI: 10.1021/acs.bioconjchem.9b00598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While the semi or total synthesis of ubiquitin or polyubiquitin conjugates has attracted a lot of attention the past decade, the preparation of small ubiquitin-like modifier (SUMO) conjugates is much less developed. We describe hereinafter some important molecular features to consider when preparing SUMO-2/3 conjugates by chemical synthesis using the native chemical ligation and extended methods. In particular, we clarify the role of the conserved cysteine residue on SUMO-2/3 domain stability and properties. Our data reveal that SUMO-2 and -3 proteins behave differently from the Cys → Ala modification with SUMO-2 being less impacted than SUMO-3, likely due to a stabilizing interaction occurring in SUMO-2 between its tail and the SUMO core domain. While the Cys → Ala modification has no effect on the enzyme-catalyzed conjugation, it shows a deleterious effect on the enzyme-catalyzed deconjugation process, especially with the SUMO-3 conjugate. Whereas it is often stated that SUMO-2 and SUMO-3 are structurally and functionally indistinguishable, here we show that these proteins have specific structural and biochemical properties. This information is important to consider when designing and preparing SUMO-2/3 conjugates, and should help in making progress in the understanding of the specific role of SUMO-2 and/or SUMO-3 modifications on protein structure and function.
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Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) , DKFZ - ZMBH Alliance, 69120 , Heidelberg , Germany
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
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Zhang Y, Hirota T, Kuwata K, Oishi S, Gramani SG, Bode JW. Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO-E2-E3 Ligase Ternary Complexes. J Am Chem Soc 2019; 141:14742-14751. [PMID: 31436980 DOI: 10.1021/jacs.9b06820] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E2 conjugating enzymes are the key catalytic actors in the transfer of ubiquitin, SUMO, and other ubiquitin-like modifiers to their substrate proteins. Their high rates of transfer and promiscuous binding complicate studies of their interactions and binding partners. To access specific, covalently linked conjugates of the SUMO E2 conjugating enzyme Ubc9, we prepared synthetic variants bearing site-specific non-native modifications including the following: (1) replacement of Cys93 to 2,3-diaminopropionic acid to form the amide-linked stable E2-SUMO conjugate, which is known to have high affinity for E3 ligases; (2) a photoreactive group (diazirine) to trap E3 ligases upon UV irradiation; and (3) an N-terminal biotin for purification and detection. To construct these Ubc9 variants in a flexible, convergent manner, we combined the three leading methods: native chemical ligation (NCL), α-ketoacid-hydroxylamine (KAHA) ligation, and serine/threonine ligation (STL). Using the synthetic proteins, we demonstrated the selective formation of Ubc9-SUMO conjugates and the trapping of an E3 ligase (RanBP2) to form the stable, covalently linked SUMO1-Ubc9-RanBP2 ternary complex. The powerful combination of ligation methods-which minimizes challenges of functional group manipulations-will enable chemical probes based on E2 conjugating enzymes to trap E3 ligases and facilitate the synthesis of other protein classes.
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Affiliation(s)
- Yinfeng Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Subramanian G Gramani
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Jeffrey W Bode
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan.,Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich 8093 , Switzerland
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30
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Zinc-Induced SUMOylation of Dynamin-Related Protein 1 Protects the Heart against Ischemia-Reperfusion Injury. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1232146. [PMID: 31428220 PMCID: PMC6679852 DOI: 10.1155/2019/1232146] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/13/2019] [Indexed: 11/22/2022]
Abstract
Background Zinc plays a role in mitophagy and protects cardiomyocytes from ischemia/reperfusion injury. This study is aimed at investigating whether SUMOylation of Drp1 is involved in the protection of zinc ion on cardiac I/R injury. Methods Mouse hearts were subjected to 30 minutes of regional ischemia followed by 2 hours of reperfusion (ischemia/reoxygenation (I/R)). Infarct size and apoptosis were assessed. HL-1 cells were subjected to 24 hours of hypoxia and 6 hours of reoxygenation (hypoxia/reoxygenation (H/R)). Zinc was given 5 min before reperfusion for 30 min. SENP2 overexpression plasmid (Flag-SENP2), Drp1 mutation plasmid (Myc-Drp1 4KR), and SUMO1 siRNA were transfected into HL-1 cells for 48 h before hypoxia. Effects of zinc on SUMO family members were analyzed by Western blotting. SUMOylation of Drp1, apoptosis and the collapse of mitochondrial membrane potential (ΔΨm), and mitophagy were evaluated. Results Compared with the control, SUMO1 modification level of proteins in the H/R decreased, while this effect was reversed by zinc. In the setting of H/R, zinc attenuated myocardial apoptosis, which was reversed by SUMO1 siRNA. Similar effects were observed in SUMO1 KO mice exposed to H/R. In addition, the dynamin-related protein 1 (Drp1) is a target protein of SUMO1. The SUMOylation of Drp1 induced by zinc regulated mitophagy and contributed to the protective effect of zinc on H/R injury. Conclusions SUMOylation of Drp1 played an essential role in zinc-induced cardio protection against I/R injury. Our findings provide a promising therapeutic approach for acute myocardial I/R injury.
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31
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Rosa MT, Abreu IA. Exploring the regulatory levels of SUMOylation to increase crop productivity. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:43-51. [PMID: 31177030 DOI: 10.1016/j.pbi.2019.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
SUMOylation is an essential post-translational modification that affects several cellular processes, from gene replication to stress response. Studies using the SUMO (de)conjugation machinery have provided evidence regarding its potential to improve crop performance and productivity under normal and adverse conditions. However, the pleiotropic effect of SUMOylation can be a disadvantage in both situations, especially when considering unpredictable environmental conditions caused by climate changes. Here, we discuss the pleiotropic effects caused by disrupting the SUMOylation machinery, and new strategies that may help to overcome pleiotropy. We propose exploring the several regulatory levels of SUMOylation recently revealed, including transcriptional, post-transcriptional regulation by alternative splicing, and post-translational modifications. These new findings may provide valuable tools to increase crop productivity.
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Affiliation(s)
- Margarida Tg Rosa
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
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32
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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33
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Kunz K, Müller S, Mendler L. Assays of SUMO protease/isopeptidase activity and function in mammalian cells and tissues. Methods Enzymol 2019; 618:389-410. [PMID: 30850061 DOI: 10.1016/bs.mie.2019.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent conjugation of the ubiquitin-related SUMO modifier to lysine residues of cellular proteins (SUMOylation) is a prevalent posttranslational modification. SUMOs are synthesized as precursor proteins that require carboxy-terminal processing prior to conjugation. Subsequently, a multistep enzymatic pathway is used for conjugation to target proteins. SUMOylation generally impacts protein-protein interactions and the assembly of multiprotein complexes. Cellular processes regulated by SUMOylation include DNA damage responses, cell cycle progression, or the control of gene expression. SUMOylation is reversible and commonly only a small fraction of a particular SUMO target is modified at a given time. Deconjugation of SUMO is catalyzed by a group of cysteine proteases termed SUMO proteases or SUMO isopeptidases. In human cells nine SUMO proteases, belonging to three separate families of cysteine proteases have been identified so far. The regulation and target specificity of individual SUMO proteases have not been dissected in detail, but the current view is that each protease controls the modification of subsets of proteins that are functionally and/or physically linked. Importantly, some SUMO proteases/isopeptidases not only function in deconjugation of SUMO from proteins, but also act in C-terminal processing of the SUMO precursors. Here we describe general methods for monitoring SUMO protease/isopeptidase activities in cell or tissue extracts.
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Affiliation(s)
- Kathrin Kunz
- Institute of Biochemistry II, Goethe University, Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University, Frankfurt, Germany.
| | - Luca Mendler
- Institute of Biochemistry II, Goethe University, Frankfurt, Germany.
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34
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van der Heden van Noort GJ, Talavera Ormeño C, van Dalen D, Ovaa H. One-Step Chemical Synthesis of Native Met1-Linked Poly-Ubiquitin Chains. Chembiochem 2019; 20:62-65. [PMID: 30264452 DOI: 10.1002/cbic.201800520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 12/11/2022]
Abstract
The enzyme-mediated construction of poly-ubiquitin (Ub) chains on target proteins leads to a variety of cellular responses and is involved in processes ranging from protein degradation to cell cycle control and immune responses. This complex post-translational modification system is under intense investigation, but generation of specific Ub chains and tools made thereof is not always trivial. We discovered that native methionine-1-linked polymeric ubiquitin chains can be constructed in a single chemical reaction. We validate correct folding and regioselective attachment of such chains using linkage specific proteases and further demonstrate that these poly-Ub chains can be converted into thioesters by the activating E1-enzyme. Subsequent ligation reactions using these in situ prepared thioesters leads to poly-ubiquitinated peptides.
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Affiliation(s)
- Gerbrand J van der Heden van Noort
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Cami Talavera Ormeño
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Duco van Dalen
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Present address: Tumor Immunology Department, Radboud Institute for Molecular Sciences, 6525 GA, Nijmegen, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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35
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Abstract
Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub-Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.
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36
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Witting KF, van der Heden van Noort GJ, Kofoed C, Talavera Ormeño C, el Atmioui D, Mulder MPC, Ovaa H. Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases. Angew Chem Int Ed Engl 2018; 57:14164-14168. [PMID: 30188611 PMCID: PMC6220884 DOI: 10.1002/anie.201809232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/04/2018] [Indexed: 12/15/2022]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a reversible post-translational modifier that is covalently attached to target proteins through an enzymatic cascade and removed by designated proteases. Abnormalities in this process, referred to as Ufmylation, have been associated with a variety of human diseases. Given this, the UFM1-specific enzymes represent potential therapeutic targets; however, understanding of their biological function has been hampered by the lack of chemical tools for activity profiling. To address this unmet need, a diversifiable platform for UFM1 activity-based probes (ABPs) utilizing a native chemical ligation (NCL) strategy was developed, enabling the generation of a variety of tools to profile both UFM1 conjugating and deconjugating enzymes. The use of the probes is demonstrated in vitro and in vivo for monitoring UFM1 enzyme reactivity, opening new research avenues.
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Affiliation(s)
- Katharina F. Witting
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Christian Kofoed
- Department of ChemistryCenter for Evolutionary Chemical BiologyUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Cami Talavera Ormeño
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Dris el Atmioui
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
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37
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Witting KF, van der Heden van Noort GJ, Kofoed C, Talavera Ormeño C, el Atmioui D, Mulder MPC, Ovaa H. Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katharina F. Witting
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Christian Kofoed
- Department of Chemistry; Center for Evolutionary Chemical Biology; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Cami Talavera Ormeño
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dris el Atmioui
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Monique P. C. Mulder
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
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38
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Cravatt BF, Hsu KL, Weerapana E. How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling. Curr Top Microbiol Immunol 2018; 420:111-130. [PMID: 30178261 PMCID: PMC7120092 DOI: 10.1007/82_2018_134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ubiquitination is a frequently occurring and very diverse posttranslational modification influencing a wide scope of cellular processes. Ubiquitin (Ub) has the unique ability to form eight different lysine-linked polymeric chains, mixed chains and engages with ubiquitin-like (Ubl) molecules. The distinct signals evoked by specific enzymes play a crucial role in, for instance, proteasome-mediated protein degradation, cell cycle regulation, and DNA damage responses. Due to the large variety of cellular functions that this posttranslational modification influences, the enzymes that construct such Ub modifications, and subsequently controle and degrade these signals, is enormous. In this chapter, we will discuss the current state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination.
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Affiliation(s)
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA USA
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39
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Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases. Angew Chem Int Ed Engl 2018; 57:8958-8962. [PMID: 29771001 PMCID: PMC6055820 DOI: 10.1002/anie.201803483] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/09/2018] [Indexed: 12/31/2022]
Abstract
SUMO is a post-translational modifier critical for cell cycle progression and genome stability that plays a role in tumorigenesis, thus rendering SUMO-specific enzymes potential pharmacological targets. However, the systematic generation of tools for the activity profiling of SUMO-specific enzymes has proven challenging. We developed a diversifiable synthetic platform for SUMO-based probes by using a direct linear synthesis method, which permits N- and C-terminal labelling to incorporate dyes and reactive warheads, respectively. In this manner, activity-based probes (ABPs) for SUMO-1, SUMO-2, and SUMO-3-specific proteases were generated and validated in cells using gel-based assays and confocal microscopy. We further expanded our toolbox with the synthesis of a K11-linked diSUMO-2 probe to study the proteolytic cleavage of SUMO chains. Together, these ABPs demonstrate the versatility and specificity of our synthetic SUMO platform for in vitro and in vivo characterization of the SUMO protease family.
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Affiliation(s)
- Monique P C Mulder
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Medicines Evaluation Board, Graadt van Roggenweg 500, 3531, AH, Utrecht, The Netherlands
| | - Katharina F Witting
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dharjath S Hameed
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dris El Atmioui
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Lindsey Lelieveld
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
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