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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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Song J, Han Z, Zheng YG. Identification and Profiling of Histone Acetyltransferase Substrates by Bioorthogonal Labeling. Curr Protoc 2022; 2:e497. [PMID: 35849593 DOI: 10.1002/cpz1.497] [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] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferases (HATs, also known as lysine acetyltransferases, KATs) catalyze acetylation of their cognate protein substrates using acetyl-CoA (Ac-CoA) as a cofactor and are involved in various physiological and pathological processes. Advances in mass spectrometry-based proteomics have allowed the discovery of thousands of acetylated proteins and the specific acetylated lysine sites. However, due to the rapid dynamics and functional redundancy of HAT activities, and the limitation of using antibodies to capture acetylated lysines, it is challenging to systematically and precisely define both the substrates and sites directly acetylated by a given HAT. Here, we describe a chemoproteomic approach to identify and profile protein substrates of individual HAT enzymes on the proteomic scale. The approach involves protein engineering to enlarge the Ac-CoA binding pocket of the HAT of interest, such that a mutant form is generated that can use functionalized acyl-CoAs as a cofactor surrogate to bioorthogonally label its protein substrates. The acylated protein substrates can then be chemoselectively conjugated either with a fluorescent probe (for imaging detection) or with a biotin handle (for streptavidin pulldown and chemoproteomic identification). This modular chemical biology approach has been successfully implemented to identify protein substrates of p300, GCN5, and HAT1, and it is expected that this method can be applied to profile and identify the sub-acetylomes of many other HAT enzymes. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling HAT protein substrates with azide/alkyne-biotin Alternate Protocol: Labeling protein substrates of HATs with azide/alkyne-TAMRA for in-gel visualization Support Protocol 1: Expression and purification of HAT mutants Support Protocol 2: Synthesis of Ac-CoA surrogates Basic Protocol 2: Streptavidin enrichment of biotinylated HAT substrates Basic Protocol 3: Chemoproteomic identification of HAT substrates Basic Protocol 4: Validation of specific HAT substrates with western blotting.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
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Song J, Ngo L, Bell K, Zheng YG. Chemoproteomic Profiling of Protein Substrates of a Major Lysine Acetyltransferase in the Native Cellular Context. ACS Chem Biol 2022; 17:1092-1102. [PMID: 35417122 DOI: 10.1021/acschembio.1c00935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The family of lysine acetyltransferases (KATs) regulates epigenetics and signaling pathways in eukaryotic cells. So far, knowledge of different KAT members contributing to the cellular acetylome is limited, which limits our understanding of biological functions of KATs in physiology and disease. Here, we found that a clickable acyl-CoA reporter, 3-azidopropanoyl CoA (3AZ-CoA), presented remarkable cell permeability and effectively acylated proteins in cells. We rationally engineered the major KAT member, histone acetyltransferase 1 (HAT1), to generate its mutant forms that displayed excellent bio-orthogonal activity for 3AZ-CoA in substrate labeling. We were able to apply the bio-orthogonal enzyme-cofactor pair combined with SILAC proteomics to achieve HAT1 substrate targeting, enrichment, and proteomic profiling in living cells. A total of 123 protein substrates of HAT1 were disclosed, underlining the multifactorial functions of this important enzyme than hitherto known. This study demonstrates the first example of utilizing bio-orthogonal reporters as a chemoproteomic strategy for substrate mapping of individual KAT isoforms in the native biological contexts.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Liza Ngo
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Kaylyn Bell
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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Sun Y, Chen Y, Peng T. A Bioorthogonal Chemical Reporter for the Detection and Identification of Protein Lactylation. Chem Sci 2022; 13:6019-6027. [PMID: 35685793 PMCID: PMC9132054 DOI: 10.1039/d2sc00918h] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022] Open
Abstract
L-Lactylation is a recently discovered post-translational modification occurring on histone lysine residues to regulate gene expression. However, the substrate scope of lactylation, especially that in non-histone proteins, remains unknown, largely...
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Affiliation(s)
- Yanan Sun
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Yanchi Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
- Institute of Chemical Biology, Shenzhen Bay Laboratory Shenzhen 518132 China
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Function and Mechanism of Novel Histone Posttranslational Modifications in Health and Disease. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6635225. [PMID: 33763479 PMCID: PMC7952163 DOI: 10.1155/2021/6635225] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Histone posttranslational modifications (HPTMs) are crucial epigenetic mechanisms regulating various biological events. Different types of HPTMs characterize and shape functional chromatin states alone or in combination, and dedicated effector proteins selectively recognize these modifications for gene expression. The dysregulation of HPTM recognition events takes part in human diseases. With the application of mass spectrometry- (MS-) based proteomics, novel histone lysine acylation has been successively discovered, e.g., propionylation, butyrylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, malonylation, succinylation, crotonylation, glutarylation, and lactylation. These nine types of modifications expand the repertoire of HPTMs and regulate chromatin remodeling, gene expression, cell cycle, and cellular metabolism. Recent researches show that HPTMs have a close connection with the pathogenesis of cancer, metabolic diseases, neuropsychiatric disorders, infertility, kidney diseases, and acquired immunodeficiency syndrome (AIDS). This review focuses on the chemical structure, sites, functions of these novel HPTMs, and underlying mechanism in gene expression, providing a glimpse into their complex regulation in health and disease.
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Lyu Z, Zhao Y, Buuh ZY, Gorman N, Goldman AR, Islam MS, Tang HY, Wang RE. Steric-Free Bioorthogonal Labeling of Acetylation Substrates Based on a Fluorine-Thiol Displacement Reaction. J Am Chem Soc 2021; 143:1341-1347. [PMID: 33433199 PMCID: PMC8300487 DOI: 10.1021/jacs.0c05605] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel bioorthogonal reaction that can selectively displace fluorine substitutions alpha to amide bonds. This fluorine-thiol displacement reaction (FTDR) allows for fluorinated cofactors or precursors to be utilized as chemical reporters, hijacking acetyltransferase-mediated acetylation both in vitro and in live cells, which cannot be achieved with azide- or alkyne-based chemical reporters. The fluoroacetamide labels can be further converted to biotin or fluorophore tags using FTDR, enabling the general detection and imaging of acetyl substrates. This strategy may lead to a steric-free labeling platform for substrate proteins, expanding our chemical toolbox for functional annotation of post-translational modifications in a systematic manner.
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Affiliation(s)
- Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Yue Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Nicole Gorman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Aaron R Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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Wu J, Zhao Y, Wang X, Kong L, Johnston LJ, Lu L, Ma X. Dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications. Crit Rev Food Sci Nutr 2020; 62:783-797. [PMID: 33043708 DOI: 10.1080/10408398.2020.1828813] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jianmin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xian Wang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Lingchang Kong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lee J. Johnston
- West Central Research & Outreach Centre, University of Minnesota, Morris, Minnesota, USA
| | - Lin Lu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Song J, Zheng YG. Bioorthogonal Reporters for Detecting and Profiling Protein Acetylation and Acylation. SLAS DISCOVERY 2019; 25:148-162. [PMID: 31711353 DOI: 10.1177/2472555219887144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein acylation, exemplified by lysine acetylation, is a type of indispensable and widespread protein posttranslational modification in eukaryotes. Functional annotation of various lysine acetyltransferases (KATs) is critical to understanding their regulatory roles in abundant biological processes. Traditional radiometric and immunosorbent assays have found broad use in KAT study but have intrinsic limitations. Designing acyl-coenzyme A (CoA) reporter molecules bearing chemoselective chemical warhead groups as surrogates of the native cofactor acetyl-CoA for bioorthogonal labeling of KAT substrates has come into a technical innovation in recent years. This chemical biology platform equips molecular biologists with empowering tools in acyltransferase activity detection and substrate profiling. In the bioorthogonal labeling, protein substrates are first enzymatically modified with a functionalized acyl group. Subsequently, the chemical warhead on the acyl chain conjugates with either an imaging chromophore or an affinity handle or any other appropriate probes through an orthogonal chemical ligation. This bioorganic strategy reformats the chemically inert acetylation and acylation marks into a chemically maneuverable functionality and generates measurable signals without recourse to radioisotopes or antibodies. It offers ample opportunities for facile sensitive detection of KAT activity with temporal and spatial resolutions as well as allows for chemoproteomic profiling of protein acetylation pertaining to specific KATs of interest on the global scale. We reviewed here the past and current advances in bioorthogonal protein acylations and highlighted their wide-spectrum applications. We also discussed the design of other related acyl-CoA and CoA-based chemical probes and their deployment in illuminating protein acetylation and acylation biology.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
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Kulkarni RA, Montgomery DC, Meier JL. Epigenetic regulation by endogenous metabolite pharmacology. Curr Opin Chem Biol 2019; 51:30-39. [PMID: 30884380 DOI: 10.1016/j.cbpa.2019.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Altered metabolite levels can drive epigenetic changes critical to development and disease. However, in many cases the specific protein-metabolite interactions that underlie this process remain enigmatic. In this review, we make the case that this fundamental missing information may be discovered by applying the tools of modern drug target validation to study endogenous metabolite pharmacology. We detail examples in which chemical proteomics has been applied to gain new insights into reversible and covalent metabolite signaling mechanisms, using acetyl-CoA and fumarate as case studies. Finally, we provide a brief survey of nascent chemical biology methods whose application to the study of endogenous metabolite pharmacology may further advance the field.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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