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Upadhyay A, Joshi V. The Ubiquitin Tale: Current Strategies and Future Challenges. ACS Pharmacol Transl Sci 2024; 7:2573-2587. [PMID: 39296276 PMCID: PMC11406696 DOI: 10.1021/acsptsci.4c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/12/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024]
Abstract
Ubiquitin (Ub) is often considered a structurally conserved protein. Ubiquitination plays a prominent role in the regulation of physiological pathways. Since the first mention of Ub in protein degradation pathways, a plethora of nonproteolytic functions of this post-translational modification have been identified and investigated in detail. In addition, several other structurally and functionally related proteins have been identified and investigated for their Ub-like structures and functions. Ubiquitination and Ub-like modifications play vital roles in modulating the pathways involved in crucial biological processes and thus affect the global proteome. In this Review, we provide a snapshot of pathways, substrates, diseases, and novel therapeutic targets that are associated with ubiquitination or Ub-like modifications. In the past few years, a large number of proteomic studies have identified pools of ubiquitinated proteins (ubiquitylomes) involved or induced in healthy or stressed conditions. These comprehensive studies involving identification of new ubiquitination substrates and sites contribute enormously to our understanding of ubiquitination in more depth. However, with the current tools, there are certain limitations that need to be addressed. We review recent technological advancements in ubiquitylomic studies and their limitations and challenges. Overall, large-scale ubiquitylomic studies contribute toward understanding global ubiquitination in the contexts of normal and disease conditions.
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Affiliation(s)
- Arun Upadhyay
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Durg, Chhattisgarh 491001, India
| | - Vibhuti Joshi
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh 201310, India
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2
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P T B, Sahu I. Decoding the ubiquitin landscape by cutting-edge ubiquitinomic approaches. Biochem Soc Trans 2024; 52:627-637. [PMID: 38572966 DOI: 10.1042/bst20230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Functional consequences of protein ubiquitination have gone far beyond the degradation regulation as was initially imagined during its discovery 40 years back. The state-of-the-art has revealed the plethora of signaling pathways that are largely regulated by ubiquitination process in eukaryotes. To no surprise, ubiquitination is often dysregulated in many human diseases, including cancer, neurodegeneration and infection. Hence it has become a major focus with high-gain research value for many investigators to unravel new proteoforms, that are the targets of this ubiquitination modification. Despite many biochemical or proteomic approaches available for ubiquitination detection, mass-spectrometry stood out to be the most efficient and transformative technology to read this complex modification script. Here in this review, we have discussed how different ubiquitin codes can be decoded qualitatively and quantitatively following various sequential proteomic approaches to date reported and indicated the current limitations with scope for improvements.
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Affiliation(s)
- Brindhavanam P T
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
| | - Indrajit Sahu
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
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3
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Xu T, Fu Q, Qingru Z, Wang Z, Liu X, Xiao S, Jiang X, Lu Y, Gong Z, Wu Y, Fang M. A simple fluorescence pyrocatechol-polyethyleneimine detection method for 3-MCPD. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:276-283. [PMID: 38113035 DOI: 10.1039/d3ay01912h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
A rapid fluorescence detection method was established for 3-monochloropropane-1,2-diol (3-MCPD). The detection system works based on the fluorescence quenching of pyrocatechol-polyethyleneimine (PCh-PEI) polymer by 3-MCPD. The fluorescence quenching ability of 3-MCPD for PCh-PEI polymer was measured at different pH and temperatures. Indeed, in the presence of 3-MCPD, the fluorescence intensity of PCh-PEI polymer solution was quenched best at 100 °C and pH 8.5. Also, the effect of different concentrations of 3-MCPD on the optical properties of the PCh-PEI polymer was examined. Under optimal experimental conditions, fluorescence detection was linear in a range of 0.08-2.0 mg per L 3-MCPD, with a calculated detection limit of 0.06 mg L-1 and a correlation coefficient of 0.9974. Concisely, the reported method has good sensitivity and can be used for the rapid detection of 3-MCPD contamination in food products.
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Affiliation(s)
- Ting Xu
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Qing Fu
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Zeng Qingru
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Zhaojie Wang
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Xin Liu
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Processing of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shensheng Xiao
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Processing of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiaoming Jiang
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan, 430040, China
| | - Yuepeng Lu
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan, 430040, China
| | - Zhiyong Gong
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Processing of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yongning Wu
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014), NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing 100022, China
| | - Min Fang
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Processing of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
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4
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Hua Z. Deciphering the protein ubiquitylation system in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6487-6504. [PMID: 37688404 DOI: 10.1093/jxb/erad354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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5
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Bashyal A, Dunham SD, Brodbelt JS. Characterization of Unbranched Ubiquitin Tetramers by Combining Ultraviolet Photodissociation with Proton Transfer Charge Reduction Reactions. Anal Chem 2023; 95:14001-14008. [PMID: 37677053 DOI: 10.1021/acs.analchem.3c02618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Polyubiquitination is an important post-translational modification (PTM) that regulates various biological functions. The linkage sites and topologies of polyubiquitination chains are important factors in determining the fate of polyubiquitinated proteins. Characterization of polyubiquitin chains is the first step in understanding the biological functions of protein ubiquitination, but it is challenging owing to the repeating nature of the ubiquitin chains and the difficulty in deciphering linkage positions. Here, we combine ultraviolet photodissociation (UVPD) mass spectrometry and gas-phase proton transfer charge reduction (PTCR) to facilitate the assignment of product ions generated from Lys6-, Lys11-, Lys29-, Lys33-, Lys48-, and Lys63-linked ubiquitin tetramers. UVPD results in extensive fragmentation of intact proteins in a manner that allows the localization of PTMs. However, UVPD mass spectra of large proteins (>30 kDa) are often congested due to the overlapping isotopic distribution of highly charged fragment ions. UVPD + PTCR improved the identification of PTM-containing fragment ions, allowing the localization of linkage sites in all six tetramers analyzed. UVPD + PTCR also increased the sequence coverage obtained from the PTM-containing fragment ions in each of the four chains of each tetramer by 7 to 44% when compared to UVPD alone.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean D Dunham
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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6
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Sahu I, Zhu H, Buhrlage SJ, Marto JA. Proteomic approaches to study ubiquitinomics. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194940. [PMID: 37121501 PMCID: PMC10612121 DOI: 10.1016/j.bbagrm.2023.194940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
As originally described some 40 years ago, protein ubiquitination was thought to serve primarily as a static mark for protein degradation. In the ensuing years, it has become clear that 'ubiquitination' is a structurally diverse and dynamic post-translational modification and is intricately involved in a myriad of signaling pathways in all eukaryote cells. And like other key pathways in the functional proteome, ubiquitin signaling is often disrupted, sometimes severely so, in human pathophysiology. As a result of its central role in normal physiology and human disease, the ubiquitination field is now represented across the full landscape of biomedical research from fundamental structural and biochemical studies to translational and clinical research. In recent years, mass spectrometry has emerged as a powerful technology for the detection and characterization of protein ubiquitination. Herein we detail qualitative and quantitative proteomic methods using a compare/contrast approach to highlight their strengths and weaknesses.
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Affiliation(s)
- Indrajit Sahu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Center for Emergent Drug Targets, USA.
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Emergent Drug Targets, USA.
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7
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Furuhata T, Devadasan Racheal PA, Murayama I, Toyoda U, Okamoto A. One-Pot, Photocontrolled Enzymatic Assembly of the Structure-Defined Heterotypic Polyubiquitin Chain. J Am Chem Soc 2023; 145:11690-11700. [PMID: 37200097 DOI: 10.1021/jacs.3c01912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterotypic polyubiquitins are an emerging class of polyubiquitins that have attracted interest because of their potential diversity of structures and physiological functions. There is an increasing demand for structure-defined synthesis of heterotypic chains to investigate the topological factors underlying the intracellular signals that are characteristically mediated by the heterotypic chain. However, the applicability of chemical and enzymatic polyubiquitin synthesis developed to date has been limited by laborious rounds of ligation and purification or by a lack of modularity of the chain structure with respect to the length and the branch position. Here, we established a one-pot, photocontrolled synthesis of structurally defined heterotypic polyubiquitin chains. We designed ubiquitin derivatives with a photolabile protecting group at a lysine residue used for polymerization. Repetitive cycles of linkage-specific enzymatic elongation and photoinduced deprotection of the protected ubiquitin units enabled stepwise addition of ubiquitins with appropriate functionalities to control the length and branching positions. The positional control of branching was achieved without isolation of intermediates, allowing one-pot synthesis of K63 triubiqutin chains and a K63/K48 heterotypic tetraubiquitin chain with defined branching positions. The present study provides a chemical platform for the efficient construction of long polyubiquitin chains with defined branch structures that will facilitate the understanding of the essential relationships between functions and structures of the heterotypic chain that have hitherto been overlooked.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Phebee Angeline Devadasan Racheal
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Iori Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Usano Toyoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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8
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Mao S, Cai X, Niu S, Wei J, Jiang N, Deng H, Wang W, Zhang J, Shen S, Ma Y, Wu X, Peng Q, Huang A, Wang D. TRIM21 promotes ubiquitination of SARS-CoV-2 nucleocapsid protein to regulate innate immunity. J Med Virol 2023; 95:e28719. [PMID: 37185839 DOI: 10.1002/jmv.28719] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
The innate immune response is the first line of host defense against viral infections, but its role in immunity against SARS-CoV-2 remains unclear. By using immunoprecipitation coupled with mass spectroscopy, we observed that the E3 ubiquitin ligase TRIM21 interacted with the SARS-CoV-2 nucleocapsid (N) protein and ubiquitinated it at Lys375 . Upon determining the topology of the TRIM21-mediated polyubiquitination chain on N protein, we then found that polyubiquitination led to tagging of the N protein for degradation by the host cell proteasome. Furthermore, TRIM21 also ubiquitinated the N proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron together with SARS-CoV and MERS-CoV variants. Herein, we propose that ubiquitylation and degradation of the SARS-CoV-2 N protein inhibited SARS-CoV-2 viral particle assembly, by which it probably involved in preventing cytokine storm. Eventually, our study has fully revealed the association between the host innate immune system and SARS-CoV-2 N protein, which may aid in developing novel SARS-CoV-2 treatment strategies.
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Affiliation(s)
- Shenglan Mao
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xuefei Cai
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Siqiang Niu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, Guangdong, China
| | - Ning Jiang
- School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Haijun Deng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wen Wang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Zhang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shimei Shen
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yuanyan Ma
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xiaoli Wu
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Qiling Peng
- School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Deqiang Wang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
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9
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van Tol BDM, van Doodewaerd BR, Lageveen-Kammeijer GSM, Jansen BC, Talavera Ormeño CMP, Hekking PJM, Sapmaz A, Kim RQ, Moutsiopoulou A, Komander D, Wuhrer M, van der Heden van Noort GJ, Ovaa H, Geurink PP. Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes. Nat Commun 2023; 14:1661. [PMID: 36966155 PMCID: PMC10039891 DOI: 10.1038/s41467-023-37363-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
Deubiquitinating enzymes are key regulators in the ubiquitin system and an emerging class of drug targets. These proteases disassemble polyubiquitin chains and many deubiquitinases show selectivity for specific polyubiquitin linkages. However, most biochemical insights originate from studies of single diubiquitin linkages in isolation, whereas in cells all linkages coexist. To better mimick this diubiquitin substrate competition, we develop a multiplexed mass spectrometry-based deubiquitinase assay that can probe all ubiquitin linkage types simultaneously to quantify deubiquitinase activity in the presence of all potential diubiquitin substrates. For this, all eight native diubiquitins are generated and each linkage type is designed with a distinct molecular weight by incorporating neutron-encoded amino acids. Overall, 22 deubiquitinases are profiled, providing a three-dimensional overview of deubiquitinase linkage selectivity over time and enzyme concentration.
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Affiliation(s)
- Bianca D M van Tol
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Bjorn R van Doodewaerd
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | | | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Paul J M Hekking
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Angeliki Moutsiopoulou
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Melbourne, Victoria, Australia
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Gerbrand J van der Heden van Noort
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands.
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10
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Singh AK, Murmu S, Krężel A. One-Step Sortase-Mediated Chemoenzymatic Semisynthesis of Deubiquitinase-Resistant Ub-Peptide Conjugates. ACS OMEGA 2022; 7:46693-46701. [PMID: 36570257 PMCID: PMC9773336 DOI: 10.1021/acsomega.2c05652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Post-translational modifications (PTMs) of proteins increase the functional diversity of the proteome and play crucial regulatory roles in cellular processes. Ubiquitination is a highly regulated and reversible PTM accomplished by a complex multistep process with the sequential action of several specific ubiquitinating (E1-E3) and deubiquitinating enzymes. The different types of ubiquitination (mono-, poly-mono-, and poly-) and the presence of several target sites in a single substrate add to its complexity, which makes the in vitro reconstitution of this ubiquitin (Ub) machinery a quite cumbersome process. Defects in components of the ubiquitination process also contribute to disease pathogenesis, especially cancer and neurodegeneration. This makes them of interest as potential therapeutic targets. Therefore, the development of efficient and reliable methods that will generate a highly homogeneous ubiquitinated peptide and protein conjugate is a topical subject area of research. In this report, we describe the development of a simple and efficient in vitro sortase-mediated chemoenzymatic strategy for semisynthesis of defined and homogeneous ubiquitin conjugates with more than 90% yield. This was achieved by engineering a sortase recognition motif in the dynamic C-terminus of ubiquitin and its conjugation to an isopeptide-linked di-Gly appended peptide LMFK(ε-GG)TEG corresponding to the ubiquitination site residues 383LMFKTEG389 of p53. The defined and homogeneous ubiquitin conjugates were also weighed for their recognition propensity by deubiquitinating enzymes. This facile semisynthesis of ubiquitin conjugates establishes a simple one-step sortase-mediated chemoenzymatic route for the synthesis of homogeneous and defined isopeptide-linked polypeptides and will help in understanding the complexity of the ubiquitination machinery as well as designing isopeptide drugs and therapeutics.
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Affiliation(s)
- Avinash K. Singh
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
- National
Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sumit Murmu
- National
Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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11
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Li Q, Zhang W. Progress in Anticancer Drug Development Targeting Ubiquitination-Related Factors. Int J Mol Sci 2022; 23:ijms232315104. [PMID: 36499442 PMCID: PMC9737479 DOI: 10.3390/ijms232315104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
Ubiquitination is extensively involved in critical signaling pathways through monitoring protein stability, subcellular localization, and activity. Dysregulation of this process results in severe diseases including malignant cancers. To develop drugs targeting ubiquitination-related factors is a hotspot in research to realize better therapy of human diseases. Ubiquitination comprises three successive reactions mediated by Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. As expected, multiple ubiquitination enzymes have been highlighted as targets for anticancer drug development due to their dominant effect on tumorigenesis and cancer progression. In this review, we discuss recent progresses in anticancer drug development targeting enzymatic machinery components.
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12
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Aziz U, Rehmani MS, Wang L, Xian B, Luo X, Shu K. Repressors: the gatekeepers of phytohormone signaling cascades. PLANT CELL REPORTS 2022; 41:1333-1341. [PMID: 35262769 DOI: 10.1007/s00299-022-02853-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Coordinated phytohormone signal transduction, in which repressors are the key players, is essential to balance plant development and stress response. In the absence of phytohormones, repressors interplay to terminate the transcription of phytohormone-responsive genes. For phytohormone signal transduction, degradation or inactivation of the repressors is a prerequisite, a process in which proteasomal degradation or protein modifications, such as phosphorylation, are involved. In this review, we summarize the various repressor proteins and their methods of regulation. In addition, we also shed light on other post-transcriptional modifications, including protein sumoylation, acetylation, methylation, and S-nitrosylation, which might be involved in repressor regulation. We conclude that repressors are the gatekeepers of phytohormone signaling, allowing transcription of phytohormone-responsive genes only when required and thus serving as a universal mechanism to conserve energy in plants. Finally, we strongly recommend that plant research should be focused further on elucidating the mechanisms regulating repressor abundance or activity, to improve our understanding of phytohormone signal transduction.
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Affiliation(s)
- Usman Aziz
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Muhammad Saad Rehmani
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Lei Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Baoshan Xian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Xiaofeng Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China.
- Research and Development Institute of Northwestern Polytechnical University, Shenzhen, 518057, China.
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13
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Editorial. J Proteomics 2022; 262:104593. [DOI: 10.1016/j.jprot.2022.104593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Steger M, Karayel Ö, Demichev V. Ubiquitinomics: history, methods and applications in basic research and drug discovery. Proteomics 2022; 22:e2200074. [PMID: 35353442 DOI: 10.1002/pmic.202200074] [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: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Martin Steger
- Evotec München GmbH, Martinsried, 82152, Germany.,Present address: Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Özge Karayel
- Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Current address: Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Vadim Demichev
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
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15
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Deol KK, Strieter ER. The ubiquitin proteoform problem. Curr Opin Chem Biol 2021; 63:95-104. [PMID: 33813043 PMCID: PMC8384647 DOI: 10.1016/j.cbpa.2021.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
The diversity of ubiquitin modifications is immense. A protein can be monoubiquitylated, multi-monoubiquitylated, and polyubiquitylated with chains varying in size and shape. Ubiquitin itself can be adorned with other ubiquitin-like proteins and smaller functional groups. Considering different combinations of post-translational modifications can give rise to distinct biological outcomes, characterizing ubiquitylated proteoforms of a given protein is paramount. In this Opinion, we review recent advances in detecting and quantifying various ubiquitin proteoforms using mass spectrometry.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
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16
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Mathieu NA, Paparisto E, Barr SD, Spratt DE. HERC5 and the ISGylation Pathway: Critical Modulators of the Antiviral Immune Response. Viruses 2021; 13:1102. [PMID: 34207696 PMCID: PMC8228270 DOI: 10.3390/v13061102] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 01/10/2023] Open
Abstract
Mammalian cells have developed an elaborate network of immunoproteins that serve to identify and combat viral pathogens. Interferon-stimulated gene 15 (ISG15) is a 15.2 kDa tandem ubiquitin-like protein (UBL) that is used by specific E1-E2-E3 ubiquitin cascade enzymes to interfere with the activity of viral proteins. Recent biochemical studies have demonstrated how the E3 ligase HECT and RCC1-containing protein 5 (HERC5) regulates ISG15 signaling in response to hepatitis C (HCV), influenza-A (IAV), human immunodeficiency virus (HIV), SARS-CoV-2 and other viral infections. Taken together, the potent antiviral activity displayed by HERC5 and ISG15 make them promising drug targets for the development of novel antiviral therapeutics that can augment the host antiviral response. In this review, we examine the emerging role of ISG15 in antiviral immunity with a particular focus on how HERC5 orchestrates the specific and timely ISGylation of viral proteins in response to infection.
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Affiliation(s)
- Nicholas A. Mathieu
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
| | - Ermela Paparisto
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON N6A 5C1, Canada; (E.P.); (S.D.B.)
| | - Stephen D. Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON N6A 5C1, Canada; (E.P.); (S.D.B.)
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
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ZHONG H, HUANG Y, JIN Y, ZHAO R. [Advances in the application of affinity separation for analyzing protein ubiquitination]. Se Pu 2021; 39:26-33. [PMID: 34227356 PMCID: PMC9274849 DOI: 10.3724/sp.j.1123.2020.07005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Indexed: 11/25/2022] Open
Abstract
Protein ubiquitination is one of the most common yet complex post-translational modifications in eukaryotes that plays an important role in various biological processes including cell signal transduction, growth, and metabolism. Disorders in the ubiquitination process have been revealed to correlate with the occurrence and development of many diseases such as neurodegenerative disease, inflammation, and cancer. Investigation of protein ubiquitination is of great importance to uncover protein functions, understand the molecular mechanisms underlying biological processes, and develop novel strategies for disease treatment. Great advances have been made toward understanding protein ubiquitination; however, it remains a challenging task due to the high diversity of ubiquitination sites and structures, as well as the dynamic nature of ubiquitination in biological processes. Protein ubiquitination occurs through the formation of a covalent bond between the carboxyl terminus of ubiquitin and the ε-amino group of a lysine residue in the substrate. As a small protein, ubiquitin itself can be further modified by another ubiquitin molecule to form homotypic or heterotypic polyubiquitin chains. There are eight sites, namely seven lysine residues (K6, K11, K27, K29, K33, K48, and K63) and one N-terminal methionine (M1), in one ubiquitin molecule that can be used to form a ubiquitin dimer. The variations in modification sites, ubiquitin chain lengths, and conformations result in differences in protein sorting, cell signaling, and function. To resolve the high complexity of protein ubiquitination, new separation approaches are required. Affinity separation based on the specific recognition between biomolecules offers high selectivity and has been employed to study the structures and functions of ubiquitination. In addition, affinity ligands are central to the separation performance. Different affinity ligands have been developed and employed for the capture and enrichment of ubiquitylated proteins. Immunoaffinity separation based on antigen-antibody interactions has been one of the most classical separation methods. Antibodies against ubiquitin or different ubiquitin linkages have been developed and widely applied for the enrichment of ubiquitylated proteins or peptides. The specific capture allows the downstream identification of endogenous ubiquitination sites via mass spectrometry and thus facilitates understanding of the roles and dynamics of polyubiquitin signals. Ubiquitin-binding domains (UBDs) are a collection of modular protein domains that can interact with ubiquitin or polyubiquitin chains. Ubiquitin-associated domains, ubiquitin-interacting motifs, and ubiquitin-binding zinc finger domains are the most frequently used UBDs. Due to the moderate affinity of UBDs toward ubiquitin or ubiquitin chains, tandem ubiquitin-binding entities (TUBEs) have been engineered with high affinities (Kd in the nanomolar range) and exhibit potential as powerful tools for ubiquitination analysis. Because of their affinity and selectivity, UBDs and TUBEs have been applied for the isolation and identification of ubiquitylated targets in cancer cells and yeasts. Compared with antibodies and UBDs, peptides are smaller in size and can be facilely synthesized via chemical approaches. The modular structure of peptides allows for de novo design and screening of artificial ubiquitin affinity ligands for targeted capture of ubiquitinated proteins. Furthermore, the polyhistidine tag at the N-terminus of ubiquitin facilitates the purification of ubiquitylated substrates using immobilized metal affinity chromatography. Considering the high complexity of biosystems, strategies combining multiple affinity ligands have emerged to further improve separation efficiency and reduce background interference. Several combinations of antibodies with UBDs, antibodies with peptidyl tags, and UBDs with peptidyl tags have been developed and proven to be effective for the analysis of protein ubiquitination. These affinity-based approaches serve as important solutions for studying the structure-activity relationship of protein ubiquitination. This review highlights the applications and recent advances in affinity separation techniques for analyzing protein ubiquitination, focusing on the methods using antibodies, UBDs, peptides, and their combinations as affinity ligands. Further, their applications in the enrichment of ubiquitin-modified substrates and the identification of ubiquitination structures are introduced. Additionally, remaining challenges in affinity separation of protein ubiquitination and perspectives are discussed.
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18
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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19
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Proteomic approaches for the profiling of ubiquitylation events and their applications in drug discovery. J Proteomics 2020; 231:103996. [PMID: 33017648 DOI: 10.1016/j.jprot.2020.103996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 09/27/2020] [Indexed: 01/23/2023]
Abstract
Protein ubiquitylation regulates almost all aspects of the biological processes including gene expression, DNA repair, cell proliferation and apoptosis in eukaryotic cells. Dysregulation of protein ubiquitylation caused by abnormal expression of enzymes in the ubiquitin system results in the onset of many diseases including cancer, neurodegenerative diseases, and metabolic syndromes. Therefore, targeting the ubiquitin system becomes a promising research area in drug discovery. Identification of protein ubiquitylation sites is critical for revealing the key ubiquitylation events associated with diseases and specific signaling pathways and for elucidating the biological functions of the specific ubiquitylation events. Many approaches that enrich for the ubiquitylated proteins and ubiquitylated peptides at the protein and peptide levels have been developed to facilitate their identification by MS. In this paper, we will review the proteomic approaches available for the identification of ubiquitylation events at the proteome scale and discuss their advantages and limitations. We will also brief the application of the profiling of ubiquitylation events in drug target discovery and in target validation for proteolysis-targeting chimera (PROTAC). Possible future research directions in this field will also be discussed. SIGNIFICANCE: Ubiquitylation plays critical roles in regulating many biological processes in eukaryotic cells. Identification of ubiquitylation sites can provide the essential information for the functional study of the specific modified substrates. Since ubiquitylated proteins have much lower abundance than non-ubiquitylated proteins, enrichment of ubiquitylated proteins or peptides is critical for their identification by MS. This review focuses on different enrichment approaches that facilitate their isolation and identification by MS and discusses the advantages and drawbacks of these approaches. The application of the profiling of ubiquitylation events in drug target discovery and future research directions will be beneficial to the research community.
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20
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Tsuchiya H, Endo A, Saeki Y. Multi-Step Ubiquitin Decoding Mechanism for Proteasomal Degradation. Pharmaceuticals (Basel) 2020; 13:ph13060128. [PMID: 32585960 PMCID: PMC7344625 DOI: 10.3390/ph13060128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
The 26S proteasome is a 2.5-MDa protease complex responsible for the selective and ATP-dependent degradation of ubiquitylated proteins in eukaryotic cells. Proteasome-mediated protein degradation accounts for ~70% of all cellular proteolysis under basal conditions, and thereby any dysfunction can lead to drastic changes in cell homeostasis. A major function of ubiquitylation is to target proteins for proteasomal degradation. Accompanied by deciphering the structural diversity of ubiquitin chains with eight linkages and chain lengths, the ubiquitin code for proteasomal degradation has been expanding beyond the best-characterized Lys48-linked ubiquitin chains. Whereas polyubiquitylated proteins can be directly recognized by the proteasome, in several cases, these proteins need to be extracted or segregated by the conserved ATPases associated with diverse cellular activities (AAA)-family ATPase p97/valosin-containing protein (VCP) complex and escorted to the proteasome by ubiquitin-like (UBL)–ubiquitin associated (UBA) proteins; these are called substrate-shuttling factors. Furthermore, proteasomes are highly mobile and are appropriately spatiotemporally regulated in response to different cellular environments and stresses. In this review, we highlight an emerging key link between p97, shuttling factors, and proteasome for efficient proteasomal degradation. We also present evidence that proteasome-containing nuclear foci form by liquid–liquid phase separation under acute hyperosmotic stress.
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21
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Li C, Han T, Guo R, Chen P, Peng C, Prag G, Hu R. An Integrative Synthetic Biology Approach to Interrogating Cellular Ubiquitin and Ufm Signaling. Int J Mol Sci 2020; 21:ijms21124231. [PMID: 32545848 PMCID: PMC7352202 DOI: 10.3390/ijms21124231] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
Global identification of substrates for PTMs (post-translational modifications) represents a critical but yet dauntingly challenging task in understanding biology and disease pathology. Here we presented a synthetic biology approach, namely ‘YESS’, which coupled Y2H (yeast two hybrid) interactome screening with PTMs reactions reconstituted in bacteria for substrates identification and validation, followed by the functional validation in mammalian cells. Specifically, the sequence-independent Gateway® cloning technique was adopted to afford simultaneous transfer of multiple hit ORFs (open reading frames) between the YESS sub-systems. In proof-of-evidence applications of YESS, novel substrates were identified for UBE3A and UFL1, the E3 ligases for ubiquitination and ufmylation, respectively. Therefore, the YESS approach could serve as a potentially powerful tool to study cellular signaling mediated by different PTMs.
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Affiliation(s)
- Chuanyin Li
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Tianting Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Rong Guo
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Peng Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Chao Peng
- University of Chinese Academy of Sciences, Beijing 100049, China;
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Gali Prag
- The Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Ronggui Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; (C.L.); (T.H.); (R.G.); (P.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 20072, China
- Correspondence:
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22
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Deol KK, Eyles SJ, Strieter ER. Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1132-1139. [PMID: 32297515 PMCID: PMC7333183 DOI: 10.1021/jasms.0c00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Misregulation of the E3 ubiquitin ligase Parkin and the kinase PINK1 underlie both inherited and idiopathic Parkinson's disease-associated neurodegeneration. Parkin and PINK1 work together to catalyze the assembly of ubiquitin chains on substrates located on the outer mitochondrial membrane to facilitate autophagic removal of damaged mitochondria through a process termed mitophagy. Quantitative measurements of Parkin-mediated chain assembly, both in vitro and on mitochondria, have revealed that chains are composed of Lys6, Lys11, Lys48, and Lys63 linkages. The combinatorial nature of these chains is further expanded by the ability of PINK1 to phosphorylate individual subunits. The precise architecture of chains produced by the coordinated action of PINK1 and Parkin, however, are unknown. Here, we demonstrate that quantitative middle-down mass spectrometry using uniformly 15N-labeled ubiquitin variants as internal standards informs on the extent of chain branching. We find that Parkin is a prolific branching enzyme in vitro. Quantitative middle-down mass spectrometry also reveals that phospho-Ser65-ubiquitin (pSer65-Ub)-a key activator of Parkin-is not incorporated into chains to a significant extent. Our results suggest that Parkin-mediated chain branching is "on-pathway", and branch points are the principal targets of the deubiquitinase USP30.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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23
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Kliza K, Husnjak K. Resolving the Complexity of Ubiquitin Networks. Front Mol Biosci 2020; 7:21. [PMID: 32175328 PMCID: PMC7056813 DOI: 10.3389/fmolb.2020.00021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.
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Affiliation(s)
- Katarzyna Kliza
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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24
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Dittmar G, Winklhofer KF. Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Front Chem 2020; 7:915. [PMID: 31998699 PMCID: PMC6966713 DOI: 10.3389/fchem.2019.00915] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
Ubiquitination of proteins is a sophisticated post-translational modification implicated in the regulation of an ever-growing abundance of cellular processes. Recent insights into different layers of complexity have shaped the concept of the ubiquitin code. Key players in determining this code are the number of ubiquitin moieties attached to a substrate, the architecture of polyubiquitin chains, and post-translational modifications of ubiquitin itself. Ubiquitination can induce conformational changes of substrates and alter their interactive profile, resulting in the formation of signaling complexes. Here we focus on a distinct type of ubiquitination that is characterized by an inter-ubiquitin linkage through the N-terminal methionine, called M1-linked or linear ubiquitination. Formation, recognition, and disassembly of linear ubiquitin chains are highly specific processes that are implicated in immune signaling, cell death regulation and protein quality control. Consistent with their role in influencing signaling events, linear ubiquitin chains are formed in a transient and spatially regulated manner, making their detection and quantification challenging.
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Affiliation(s)
- Gunnar Dittmar
- Proteomics of Cellular Signalling, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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25
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Mendes ML, Fougeras MR, Dittmar G. Analysis of ubiquitin signaling and chain topology cross-talk. J Proteomics 2020; 215:103634. [PMID: 31918034 DOI: 10.1016/j.jprot.2020.103634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022]
Abstract
Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.
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Affiliation(s)
- Marta L Mendes
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Miriam R Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg.
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26
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Cundiff MD, Hurley CM, Wong JD, Boscia JA, Bashyal A, Rosenberg J, Reichard EL, Nassif ND, Brodbelt JS, Kraut DA. Ubiquitin receptors are required for substrate-mediated activation of the proteasome's unfolding ability. Sci Rep 2019; 9:14506. [PMID: 31601863 PMCID: PMC6787058 DOI: 10.1038/s41598-019-50857-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/20/2019] [Indexed: 12/05/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for the bulk of protein degradation in eukaryotic cells, but the factors that cause different substrates to be unfolded and degraded to different extents are still poorly understood. We previously showed that polyubiquitinated substrates were degraded with greater processivity (with a higher tendency to be unfolded and degraded than released) than ubiquitin-independent substrates. Thus, even though ubiquitin chains are removed before unfolding and degradation occur, they affect the unfolding of a protein domain. How do ubiquitin chains activate the proteasome’s unfolding ability? We investigated the roles of the three intrinsic proteasomal ubiquitin receptors - Rpn1, Rpn10 and Rpn13 - in this activation. We find that these receptors are required for substrate-mediated activation of the proteasome’s unfolding ability. Rpn13 plays the largest role, but there is also partial redundancy between receptors. The architecture of substrate ubiquitination determines which receptors are needed for maximal unfolding ability, and, in some cases, simultaneous engagement of ubiquitin by multiple receptors may be required. Our results suggest physical models for how ubiquitin receptors communicate with the proteasomal motor proteins.
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Affiliation(s)
- Mary D Cundiff
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Department of Biological Sciences, Carnegie Mellon University, Mellon Institute of Industrial Research, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Christina M Hurley
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Jeremy D Wong
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Joseph A Boscia
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jake Rosenberg
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eden L Reichard
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA, 18015, USA
| | - Nicholas D Nassif
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Bronx-Lebanon Hospital Center, 1650 Grand Concourse, Bronx, NY, 10457, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
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27
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Insights into ubiquitin chain architecture using Ub-clipping. Nature 2019; 572:533-537. [PMID: 31413367 DOI: 10.1038/s41586-019-1482-y] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/17/2019] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is a multi-functional post-translational modification that affects all cellular processes. Its versatility arises from architecturally complex polyubiquitin chains, in which individual ubiquitin moieties may be ubiquitinated on one or multiple residues, and/or modified by phosphorylation and acetylation1-3. Advances in mass spectrometry have enabled the mapping of individual ubiquitin modifications that generate the ubiquitin code; however, the architecture of polyubiquitin signals has remained largely inaccessible. Here we introduce Ub-clipping as a methodology by which to understand polyubiquitin signals and architectures. Ub-clipping uses an engineered viral protease, Lbpro∗, to incompletely remove ubiquitin from substrates and leave the signature C-terminal GlyGly dipeptide attached to the modified residue; this simplifies the direct assessment of protein ubiquitination on substrates and within polyubiquitin. Monoubiquitin generated by Lbpro∗ retains GlyGly-modified residues, enabling the quantification of multiply GlyGly-modified branch-point ubiquitin. Notably, we find that a large amount (10-20%) of ubiquitin in polymers seems to exist as branched chains. Moreover, Ub-clipping enables the assessment of co-existing ubiquitin modifications. The analysis of depolarized mitochondria reveals that PINK1/parkin-mediated mitophagy predominantly exploits mono- and short-chain polyubiquitin, in which phosphorylated ubiquitin moieties are not further modified. Ub-clipping can therefore provide insight into the combinatorial complexity and architecture of the ubiquitin code.
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28
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Abstract
The small protein ubiquitin and its multiple polymers are encountered free in cells and as post-translational modifications on all proteins. Different polyubiquitin three dimensional structures are shown to correlate uniquely with different cellular functions as part of the diverse ubiquitin signaling. At the same time, this multiplicity of structures provides serious challenges to the analytical biochemist. Globally applicable strategies are presented here for the analyses of polyubiquitins and of ubiquitinated proteins, which take advantage of the speed, specificity and sensitivity of top-down tandem mass spectrometry. Particular attention is given to the supervised interpretation of fragmentation as revealed in the MS/MS spectra of these branched proteins. The strategy is compatible with any MS activation technology, is applicable to all polyubiquitin linkage and chain types, can be extended to ubiquitin-like proteins, and will be compatible with and enhanced by continuing advances in LC-MS/MS instrumentation and interpretation software.
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Affiliation(s)
- Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States.
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29
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The Role of Ubiquitination in Regulating Embryonic Stem Cell Maintenance and Cancer Development. Int J Mol Sci 2019; 20:ijms20112667. [PMID: 31151253 PMCID: PMC6600158 DOI: 10.3390/ijms20112667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/19/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
Ubiquitination regulates nearly every aspect of cellular events in eukaryotes. It modifies intracellular proteins with 76-amino acid polypeptide ubiquitin (Ub) and destines them for proteolysis or activity alteration. Ubiquitination is generally achieved by a tri-enzyme machinery involving ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases (E3). E1 activates Ub and transfers it to the active cysteine site of E2 via a transesterification reaction. E3 coordinates with E2 to mediate isopeptide bond formation between Ub and substrate protein. The E1-E2-E3 cascade can create diverse types of Ub modifications, hence effecting distinct outcomes on the substrate proteins. Dysregulation of ubiquitination results in severe consequences and human diseases. There include cancers, developmental defects and immune disorders. In this review, we provide an overview of the ubiquitination machinery and discuss the recent progresses in the ubiquitination-mediated regulation of embryonic stem cell maintenance and cancer biology.
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30
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Maspero E, Fajner V, Weber J, Polo S. Detection of ubiquitinated targets in mammalian and Drosophila models. Methods Enzymol 2019; 619:293-318. [PMID: 30910026 DOI: 10.1016/bs.mie.2018.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this chapter, we describe techniques to detect ubiquitination events occurring in vivo. We focus on methodologies capable of preserving and detecting target protein ubiquitination in physiological conditions, without overexpressing a tagged version of ubiquitin. We provide detailed protocols for mammalian and Drosophila melanogaster systems using linkage-specific antibodies against ubiquitin. We analyze immunoblotting and immunofluorescence approaches as well as an ELISA-based quantitative approach, which allows comparing more samples and conditions. Finally, we describe the use of in vitro ubiquitination assays with purified proteins that allows a direct analysis of the molecular mechanisms behind specific E3 activity.
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Affiliation(s)
- Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.
| | - Valentina Fajner
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Janine Weber
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy; Dipartimento di oncologia ed emato-oncologia, Universita' degli Studi di Milano, Milan, Italy.
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31
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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32
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Sidoli S. Middle-Down MS is Ready to Answer Complex Questions in Chromatin Biology. Proteomics 2018; 18:e1800131. [DOI: 10.1002/pmic.201800131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Simone Sidoli
- Epigenetics Institute; Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia PA 19104 USA
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33
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Tsuchiya H, Burana D, Ohtake F, Arai N, Kaiho A, Komada M, Tanaka K, Saeki Y. Ub-ProT reveals global length and composition of protein ubiquitylation in cells. Nat Commun 2018; 9:524. [PMID: 29410401 PMCID: PMC5802829 DOI: 10.1038/s41467-018-02869-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/02/2018] [Indexed: 01/09/2023] Open
Abstract
Protein ubiquitylation regulates diverse cellular processes via distinct ubiquitin chains that differ by linkage type and length. However, a comprehensive method for measuring these properties has not been developed. Here we describe a method for assessing the length of substrate-attached polyubiquitin chains, "ubiquitin chain protection from trypsinization (Ub-ProT)." Using Ub-ProT, we found that most ubiquitylated substrates in yeast-soluble lysate are attached to chains of up to seven ubiquitin molecules. Inactivation of the ubiquitin-selective chaperone Cdc48 caused a dramatic increase in chain lengths on substrate proteins, suggesting that Cdc48 complex terminates chain elongation by substrate extraction. In mammalian cells, we found that ligand-activated epidermal growth factor receptor (EGFR) is rapidly modified with K63-linked tetra- to hexa-ubiquitin chains following EGF treatment in human cells. Thus, the Ub-ProT method can contribute to our understanding of mechanisms regulating physiological ubiquitin chain lengths and composition.
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Affiliation(s)
- Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Daocharad Burana
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-B16 Nagatsuta, Midori, Yokohama, 226-8501, Japan
| | - Fumiaki Ohtake
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Naoko Arai
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Ai Kaiho
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-B16 Nagatsuta, Midori, Yokohama, 226-8501, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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34
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Sanders JD, Greer SM, Brodbelt JS. Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics. Anal Chem 2017; 89:11772-11778. [DOI: 10.1021/acs.analchem.7b03396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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35
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Abstract
In this issue of Molecular Cell, Zhang et al. (2017) systematically identify proteins interacting with all possible di-ubiquitin linkages, thus providing a catalog of readers of the ubiquitin code.
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Affiliation(s)
- Gunnar Dittmar
- Proteome and Genome Research, Luxembourg Institute of Health, 1a Rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13092 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
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36
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Kim JY, Song JT, Seo HS. Post-translational modifications of Arabidopsis E3 SUMO ligase AtSIZ1 are controlled by environmental conditions. FEBS Open Bio 2017; 7:1622-1634. [PMID: 28979848 PMCID: PMC5623694 DOI: 10.1002/2211-5463.12309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 01/04/2023] Open
Abstract
Sumoylation regulates numerous cellular functions in plants as well as in other eukaryotic systems. However, the regulatory mechanisms controlling E3 small ubiquitin‐related modifier (SUMO) ligase are not well understood. Here, post‐translational modification of the Arabidopsis E3 SUMO ligase AtSIZ1 was shown to be specifically controlled by abiotic stresses. AtSIZ1 ubiquitination was induced by exposure to heat stress in transgenic plants overexpressing the E3 ubiquitin ligase COP1. In addition, AtSIZ1 ubiquitination was strongly enhanced in transgenic plants overexpressing SUMO isopeptidase ESD4 under heat stress. By contrast, drought stress induced sumoylation rather than ubiquitination of AtSIZ1 and sumoylated forms of AtSIZ1 accumulated in esd4 and cop1–4 mutants. Moreover, siz1 mutants were found to be tolerant to heat and drought stresses. Taken together, these results indicate that ubiquitination and sumoylation of AtSIZ1 in response to abiotic stresses depend on the activities of COP1 and ESD4 and that the activity and stability of AtSIZ1 can be specifically controlled by different abiotic stresses.
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Affiliation(s)
- Joo Yong Kim
- Department of Plant ScienceResearch Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding InstituteSeoul National UniversityKorea
| | - Jong Tae Song
- School of Applied BiosciencesKyungpook National UniversityDaeguKorea
| | - Hak Soo Seo
- Department of Plant ScienceResearch Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding InstituteSeoul National UniversityKorea.,Bio-MAX InstituteSeoul National UniversityKorea
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37
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Wagner ND, Clemmer DE, Russell DH. ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin. Anal Chem 2017; 89:10094-10103. [DOI: 10.1021/acs.analchem.7b02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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38
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Crowe SO, Rana ASJB, Deol KK, Ge Y, Strieter ER. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo. Anal Chem 2017; 89:4428-4434. [PMID: 28291339 PMCID: PMC5541364 DOI: 10.1021/acs.analchem.6b03675] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ubiquitin (Ub) has a broad functional range that has been ascribed to the formation of an array of polymeric ubiquitin chains. Understanding the precise roles of ubiquitin chains, however, is difficult due to their complex chain topologies. Branched ubiquitin chains are particularly challenging, as multiple modifications on a single ubiquitin preclude the use of standard bottom-up proteomic approaches. Developing methods to overcome these challenges is crucial considering evidence suggesting branched chains regulate the stability of proteins. In this study, we employ Ubiquitin Chain Enrichment Middle-down Mass Spectrometry (UbiChEM-MS) to identify branched chains that cannot be detected using bottom-up proteomic methods. Specifically, we employ tandem ubiquitin binding entities (TUBEs) and the K29-selective Npl4 Zinc Finger 1 (NZF1) domain from the deubiquitinase TRABID to enrich for chains from human cells. Minimal trypsinolysis followed by high resolution mass spectrometric analysis reveals that Ub chain branching can indeed be detected using both Ub binding domains (UBDs) tested at endogenous levels. We find that ∼1% of chains isolated with TUBEs contain Ub branch points, with this value rising to ∼4% after proteasome inhibition. Electron-transfer dissociation (ETD) analysis indicates the presence of K48 in these branched chains. The use of the NZF1 domain reveals that ∼4% of the isolated chains contain branch points with no apparent dependence on proteasome inhibition. Our results demonstrate an effective strategy for detecting and characterizing the dynamics of branched conjugates under different cellular conditions.
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Affiliation(s)
- Sean O. Crowe
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ambar S. J. B. Rana
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirandeep K. Deol
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Eric R. Strieter
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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39
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Zhu J, Zhuang T, Yang H, Li X, Liu H, Wang H. Atypical ubiquitin ligase RNF31: the nuclear factor modulator in breast cancer progression. BMC Cancer 2016; 16:538. [PMID: 27460922 PMCID: PMC4962416 DOI: 10.1186/s12885-016-2575-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 07/18/2016] [Indexed: 12/16/2022] Open
Abstract
Breast cancer causes the No.1 women cancer prevalence and the No.2 women cancer mortality worldwide. Nuclear receptor/transcriptional factor signaling is aberrant and plays important roles in breast cancer pathogenesis and evolution, such as estrogen receptor α (ERα/ESR1), tumor protein p53 (p53/TP53) and Nuclear factor kappa B (NFκB). About 60–70 % of breast tumors are ERα positive, while approximate 70 % of breast tumors are P53 wild type. Recent studies indicate that nuclear receptors/transcriptional factors could be tightly controlled through protein post-translational modification. The nuclear receptors/transcriptional factors could endure several types of modifications, including phosphorylation, acetylation and ubiquitination. Compared with the other two types of modifications, ubiquitination was mostly linked to protein degradation process, while few researches focused on the functional changes of the target proteins. Until recent years, ubiquitination process is no longer regarded as merely a protein degradation process, but aslo treated as one kind of modification signal. As an atypical E3 ubiquitin ligase, RNF31 was previously found to facilitate NFκB signaling transduction through linear ubiquitination on IKKγ(IκB kinase γ). Our previous studies showed important regulatory functions of RNF31 in controlling important oncogenic pathways in breast cancer, such as ERα and p53. This review highlights recent discoveries on RNF31 functions in nuclear factor modifications, breast cancer progression and possible therapeutic inhibitors targeting RNF31.
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Affiliation(s)
- Jian Zhu
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China. .,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ting Zhuang
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China
| | - Huijie Yang
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China
| | - Xin Li
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China
| | - Huandi Liu
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China
| | - Hui Wang
- Research Center for Immunology, School of Laboratory Medicine, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan Province, People's Republic of China.
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40
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Lee AE, Geis-Asteggiante L, Dixon EK, Kim Y, Kashyap TR, Wang Y, Fushman D, Fenselau C. Preparing to read the ubiquitin code: characterization of ubiquitin trimers by top-down mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:315-21. [PMID: 27041663 PMCID: PMC4909354 DOI: 10.1002/jms.3759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 05/12/2023]
Abstract
The profound effects of ubiquitination on the movement and processing of cellular proteins depend exquisitely on the structures of monoubiquitin and polyubiquitin modifications. Unconjugated polyubiquitins also have a variety of intracellular functions. Structures and functions are not well correlated yet, because the structures of polyubiquitins and polyubiquitin modifications of proteins are difficult to decipher. We are moving towards a robust strategy to provide that structural information. In this report electron transfer dissociation mass spectra of six synthetic ubiquitin trimers (multiply branched proteins with molecular masses exceeding 25,600 Da) are examined using an Orbitrap Fusion Lumos instrument to determine how top-down mass spectrometry can characterize the chain topology and linkage sites in a single, facile workflow. The efficacy of this method relies on the formation, detection, and interpretation of extensive fragmentation.
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Affiliation(s)
- Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Emma K Dixon
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Yeji Kim
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Tanuja R Kashyap
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Yan Wang
- Proteomics Core Facility, University of Maryland, College Park, MD, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
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41
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Abstract
Protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. Once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modifications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the 'ubiquitin code'. Ubiquitin can be ubiquitinated on seven lysine (Lys) residues or on the N-terminus, leading to polyubiquitin chains that can encompass complex topologies. Alternatively or in addition, ubiquitin Lys residues can be modified by ubiquitin-like molecules (such as SUMO or NEDD8). Finally, ubiquitin can also be acetylated on Lys, or phosphorylated on Ser, Thr or Tyr residues, and each modification has the potential to dramatically alter the signaling outcome. While the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. We here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. We then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation.
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Affiliation(s)
- Kirby N Swatek
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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42
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Beaudette P, Popp O, Dittmar G. Proteomic techniques to probe the ubiquitin landscape. Proteomics 2015; 16:273-87. [PMID: 26460060 DOI: 10.1002/pmic.201500290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/03/2015] [Accepted: 10/06/2015] [Indexed: 01/06/2023]
Abstract
Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct signals, either by adding a single ubiquitin or forming a chain of ubiquitins on the target protein. The enzymatic cascade associated with the cellular process determines the nature of the modification. Numerous efforts have been made for the identification of ubiquitin acceptor sites in the target proteins using genetic, biochemical or MS-based proteomic methods, such as affinity-based enrichment of ubiquitinated proteins, and antibody-based enrichment of modified peptides. Modern instrumentation enables quantitative MS strategies to identify and characterize hundreds of ubiquitin substrates in a single analysis making it the dominant method for ubiquitin site detection. Characterization of the interubiquitin connectivity in ubiquitin polymers has also moved into focus, with the field of targeted proteomics techniques proving invaluable for identifying and quantifying linkage types found in such polyubiquitin chains. This review seeks to provide an overview of the many MS-based proteomics techniques available for exploring this dynamic field.
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Affiliation(s)
- Patrick Beaudette
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Oliver Popp
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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43
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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44
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Ube2s regulates Sox2 stability and mouse ES cell maintenance. Cell Death Differ 2015; 23:393-404. [PMID: 26292759 DOI: 10.1038/cdd.2015.106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/21/2015] [Accepted: 07/01/2015] [Indexed: 11/09/2022] Open
Abstract
Sox2 has a critical role in embryonic stem (ES) cell maintenance and differentiation. Interestingly, its activity is highly dosage-dependent. Although transcriptional regulation of Sox2 has been extensively studied, the mechanisms orchestrating its degradation remain unclear. In this study, we identified ubiquitin-conjugating enzyme E2S (Ube2s) as a novel effector for Sox2 protein degradation. Ube2s mediates K11-linked polyubiquitin chain formation at the Sox2-K123 residue, thus marking it for proteasome-mediated degradation. Besides its role in fine-tuning the precise level of Sox2, Ube2s reinforces the self-renewing and pluripotent state of ES cells. Importantly, it also represses Sox2-mediated ES cell differentiation toward the neural ectodermal lineage.
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45
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Abstract
Ubiquitin (UB)-driven signaling systems permeate biology, and are often integrated with other types of post-translational modifications (PTMs), including phosphorylation. Flux through such pathways is dictated by the fractional stoichiometry of distinct modifications and protein assemblies as well as the spatial organization of pathway components. Yet, we rarely understand the dynamics and stoichiometry of rate-limiting intermediates along a reaction trajectory. Here, we review how quantitative proteomic tools and enrichment strategies are being used to quantify UB-dependent signaling systems, and to integrate UB signaling with regulatory phosphorylation events, illustrated with the PINK1/PARKIN pathway. A key feature of ubiquitylation is that the identity of UB chain linkage types can control downstream processes. We also describe how proteomic and enzymological tools can be used to identify and quantify UB chain synthesis and linkage preferences. The emergence of sophisticated quantitative proteomic approaches will set a new standard for elucidating biochemical mechanisms of UB-driven signaling systems.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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46
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Sweredoski MJ, Moradian A, Raedle M, Franco C, Hess S. High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics. Anal Chem 2015; 87:8360-6. [DOI: 10.1021/acs.analchem.5b01542] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael J. Sweredoski
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Annie Moradian
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Matthias Raedle
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
- Hochschule Weihenstephan-Triesdorf, University of Applied Sciences, Faculty of Biotechnology and Bioinformatic, Am Hofgarten 4, 85354 Freising, Germany
| | - Catarina Franco
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sonja Hess
- Proteome
Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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47
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Burke MC, Wang Y, Lee AE, Dixon EK, Castaneda CA, Fushman D, Fenselau C. Unexpected trypsin cleavage at ubiquitinated lysines. Anal Chem 2015; 87:8144-8. [PMID: 26182167 PMCID: PMC4599693 DOI: 10.1021/acs.analchem.5b01960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Unexpected tryptic cleavage has been characterized at modified K48 residues in polyubiquitins. In particular, the tryptic products of all seven of the lysine-linked dimers of ubiquitin and of three trimers-linear Ub-(48)Ub-(48)Ub, linear Ub-(63)Ub-(63)Ub, and the branched trimer [Ub]2-(6,48)Ub-have been analyzed. In addition to the peptide products expected under commonly used tryptic conditions, we observe that peptides are formed with an unexpected ε-glycinylglycinyl-Lys carboxyl terminus when the site of linkage is Lys48. Trypsin from three different commercial sources exhibited this aberration. Initial cleavage at R74 is proposed in a distal ubiquitin to produce a glycinylglycinyl-lysine residue which is bound by trypsin.
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48
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Tsiatsiani L, Heck AJR. Proteomics beyond trypsin. FEBS J 2015; 282:2612-26. [PMID: 25823410 DOI: 10.1111/febs.13287] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/13/2022]
Abstract
Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.
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Affiliation(s)
- Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
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49
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Cannon JR, Martinez-Fonts K, Robotham SA, Matouschek A, Brodbelt JS. Top-down 193-nm ultraviolet photodissociation mass spectrometry for simultaneous determination of polyubiquitin chain length and topology. Anal Chem 2015; 87:1812-20. [PMID: 25559986 PMCID: PMC4318624 DOI: 10.1021/ac5038363] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/01/2015] [Indexed: 11/29/2022]
Abstract
Protein ubiquitin modifications present a vexing analytical challenge, because of the dynamic changes in the site of modification on the substrate, the number of ubiquitin moieties attached, and the diversity of linkage patterns in which they are attached. Presented here is a method to confidently assign size and linkage type of polyubiquitin modifications. The method combines intact mass measurement to determine the number of ubiquitin moieties in the chain with backbone fragmentation by 193-nm ultraviolet photodissociation (UVPD) to determine the linkage pattern. UVPD fragmentation of proteins leads to reproducible backbone cleavage at almost every inter-residue position, and in polyubiquitin chains, the N-terminally derived fragments from each constituent monomer are identical, up to the site of conjugation. The N-terminal ubiquitin fragment ions are superimposed to create a diagnostic pattern that allows easy recognition of the dominant chain linkages. The method is demonstrated by achieving almost-complete fragmentation of monoubiquitin and then, subsequently, fragmentation of dimeric, tetrameric, and longer Lys48- and Lys63-linked ubiquitin chains. The utility of the method for the analysis of mixed linkage chains is confirmed for mixtures of Lys48 and Lys63 tetramers with known relative concentrations and for an in vitro-formulated ubiquitin chain attached to a substrate protein.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
| | - Kirby Martinez-Fonts
- Department
of Molecular Biosciences, University of
Texas, Austin, Texas 78712, United
States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
| | - Andreas Matouschek
- Department
of Molecular Biosciences, University of
Texas, Austin, Texas 78712, United
States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
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50
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Deubiquitinase-based analysis of ubiquitin chain architecture using Ubiquitin Chain Restriction (UbiCRest). Nat Protoc 2015; 10:349-361. [PMID: 25633630 DOI: 10.1038/nprot.2015.018] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (multiple linkage types per polymer) chains poses significant problems for biochemical analysis. Here we describe UbiCRest, in which substrates (ubiquitinated proteins or polyubiquitin chains) are treated with a panel of linkage-specific deubiquitinating enzymes (DUBs) in parallel reactions, followed by gel-based analysis. UbiCRest can be used to show that a protein is ubiquitinated, to identify which linkage type(s) are present on polyubiquitinated proteins and to assess the architecture of heterotypic polyubiquitin chains. DUBs used in UbiCRest can be obtained commercially; however, we include details for generating a toolkit of purified DUBs and for profiling their linkage preferences in vitro. UbiCRest is a qualitative method that yields insights into ubiquitin chain linkage types and architecture within hours, and it can be performed on western blotting quantities of endogenously ubiquitinated proteins.
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