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Zhao H, Han Y, Zhou P, Guan H, Gao S. Protein lysine crotonylation in cellular processions and disease associations. Genes Dis 2024; 11:101060. [PMID: 38957707 PMCID: PMC11217610 DOI: 10.1016/j.gendis.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 05/05/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2024] Open
Abstract
Protein lysine crotonylation (Kcr) is one conserved form of posttranslational modifications of proteins, which plays an important role in a series of cellular physiological and pathological processes. Lysine ε-amino groups are the primary sites of such modification, resulting in four-carbon planar lysine crotonylation that is structurally and functionally distinct from the acetylation of these residues. High levels of Kcr modifications have been identified on both histone and non-histone proteins. The present review offers an update on the research progression regarding protein Kcr modifications in biomedical contexts and provides a discussion of the mechanisms whereby Kcr modification governs a range of biological processes. In addition, given the importance of protein Kcr modification in disease onset and progression, the potential viability of Kcr regulators as therapeutic targets is elucidated.
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Affiliation(s)
- Hongling Zhao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Han
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pingkun Zhou
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
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2
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Yan W, Zhang Y, Dai Y, Ge J. Application of crotonylation modification in pan-vascular diseases. J Drug Target 2024:1-9. [PMID: 38922829 DOI: 10.1080/1061186x.2024.2372316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Pan-vascular diseases, based on systems biology theory, explore the commonalities and individualities of important target organs such as cardiovascular, cerebrovascular and peripheral blood vessels, starting from the systemic and holistic aspects of vascular diseases. The purpose is to understand the interrelationships and results between them, achieve vascular health or sub-health, and comprehensively improve the physical and mental health of the entire population. Post-translational modification (PTM) is an important part of epigenetics, including phosphorylation, acetylation, ubiquitination, methylation, etc., playing a crucial role in the pan-vascular system. Crotonylation is a novel type of PTM that has made significant progress in the research of pan-vascular related diseases in recent years. Based on the review of previous studies, this article summarises the various regulatory factors of crotonylation, physiological functions and the mechanisms of histone and non-histone crotonylation in regulating pan-vascular related diseases to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment and the value of clinical translation.
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Affiliation(s)
- Wendi Yan
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
| | - Yang Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Yuxiang Dai
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Junbo Ge
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
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3
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Li D, Lin L, Xu F, Feng T, Tao Y, Miao H, Yang F. Protein crotonylation: Basic research and clinical diseases. Biochem Biophys Rep 2024; 38:101694. [PMID: 38586826 PMCID: PMC10997999 DOI: 10.1016/j.bbrep.2024.101694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Crotonylation is an importantly conserved post-translational modification, which is completely different from acetylation. In recent years, it has been confirmed that crotonylation occurs on histone and non-histone. Crotonylated Histone primarily affects gene expression through transcriptional regulation, while non-histone Crotonylation mainly regulates protein functions including protein activity, localization, and stability, as well as protein-protein interactions. The change in protein expression and function will affect the physiological process of cells and even cause disease. Reviewing previous studies, this article summarizes the mechanisms of histone and non-histone crotonylation in regulating diseases and cellular physiological processes to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment.
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Affiliation(s)
- Dongling Li
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Ling Lin
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Fan Xu
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Tianlin Feng
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yang Tao
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400000, China
| | - Hongming Miao
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Fan Yang
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Biochemistry and Molecular Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
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4
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He Y, Xie Y, Zhou T, Li D, Cheng X, Yang P, Luo C, Liu Y, Guo M, Wan Q, Yan P, Gao C, Zhang YY, Sun XD, Xu Y, Huang W. Sodium Crotonate Alleviates Diabetic Kidney Disease Partially Via the Histone Crotonylation Pathway. Inflammation 2024:10.1007/s10753-024-02047-w. [PMID: 38822951 DOI: 10.1007/s10753-024-02047-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Diabetic kidney disease (DKD) is a common microvascular complication of diabetes, inflammation and fibrosis play an important role in its progression. Histone lysine crotonylation (Kcr) was first identified as a new type of post-translational modification in 2011. In recent years, prominent progress has been made in the study of sodium crotonate (NaCr) and histone Kcr in kidney diseases. However, the effects of NaCr and NaCr-induced Kcr on DKD remain unclear. In this study, db/db mice and high glucose-induced human tubular epithelial cells (HK-2) were used respectively, and exogenous NaCr and crotonoyl-coenzyme A (Cr-CoA) as intervention reagents, histone Kcr and DKD-related indicators were detected. The results confirmed that NaCr had an antidiabetic effect and decreased blood glucose and serum lipid levels and alleviated renal function and DKD-related inflammatory and fibrotic damage. NaCr also induced histone Kcr and histone H3K18 crotonylation (H3K18cr). However, NaCr and Cr-CoA-induced histone Kcr and protective effects were reversed by inhibiting the activity of Acyl-CoA synthetase short-chain family member 2 (ACSS2) or histone acyltransferase P300 in vitro. In summary, our data reveal that NaCr may mitigate DKD via an antidiabetic effect as well as through ACSS2 and P300-induced histone Kcr, suggesting that Kcr may be the potential molecular mechanism and prevention target of DKD.
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Affiliation(s)
- Yanqiu He
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Yumei Xie
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Tingting Zhou
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Dongze Li
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Xi Cheng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Changfang Luo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Yijun Liu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Qin Wan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Pijun Yan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Chenlin Gao
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China
| | - Yuan-Yuan Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Xiao-Dong Sun
- West China School of Basic Medical Sciences & Forensic Medicine, Chengdu, 610041, China
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China.
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China.
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, Sichuan, 646000, China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, Sichuan, 646000, China.
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, 646000, China.
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Xie JY, Ju J, Zhou P, Chen H, Wang SC, Wang K, Wang T, Chen XZ, Chen YC, Wang K. The mechanisms, regulations, and functions of histone lysine crotonylation. Cell Death Discov 2024; 10:66. [PMID: 38331935 PMCID: PMC10853258 DOI: 10.1038/s41420-024-01830-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Histone lysine crotonylation (Kcr) is a new acylation modification first discovered in 2011, which has important biological significance for gene expression, cell development, and disease treatment. In the past over ten years, numerous signs of progress have been made in the research on the biochemistry of Kcr modification, especially a series of Kcr modification-related "reader", "eraser", and "writer" enzyme systems are identified. The physiological function of crotonylation and its correlation with development, heredity, and spermatogenesis have been paid more and more attention. However, the development of disease is usually associated with abnormal Kcr modification. In this review, we summarized the identification of crotonylation modification, Kcr-related enzyme system, biological functions, and diseases caused by abnormal Kcr. This knowledge supplies a theoretical basis for further exploring the function of crotonylation in the future.
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Affiliation(s)
- Jing-Yi Xie
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Jie Ju
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
- Department of Physiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, 261053, China.
| | - Ping Zhou
- State Key Laboratory of Cardiovascular Disease, Heart Failure center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100037, China
| | - Hao Chen
- Department of Physiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Shao-Cong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Tao Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Xin-Zhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Yan-Chun Chen
- Neurologic Disorders and Regenerative Repair Laboratory, Shandong Second Medical University, Weifang, 261053, China.
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
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Wang W, Shi W, Wang Y, Yang Y, Li P, Zeng Z, Hu W, Chen Y, Tang D, Dai Y. Systematic proteomics profiling of lysine crotonylation of the lung at Pseudoglandular and Canalicular phases in human fetus. Proteome Sci 2023; 21:22. [PMID: 38041078 PMCID: PMC10691156 DOI: 10.1186/s12953-023-00215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/28/2023] [Indexed: 12/03/2023] Open
Abstract
Lung tissue is an important organ of the fetus, and genomic research on its development has improved our understanding of the biology of this tissue. However, the proteomic research of developing fetal lung tissue is still very scarce. We conducted comprehensive analysis of two developmental stages of fetal lung tissue of proteomics. It showed the developmental characteristics of lung tissue, such as the down-regulation of metabolism-related protein expression, the up-regulation of cell cycle-related proteins, and the regulation in proteins and pathways related to lung development. In addition, we also discovered some key core proteins related to lung development, and provided some key crotonylation modification sites that regulation during lung tissue development. Our comprehensive analysis of lung proteomics can provide a more comprehensive understanding of the developmental status of lung tissue, and provide a certain reference for future research and epigenetics of lung tissue.
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Affiliation(s)
- Wei Wang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wei Shi
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern, University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yinglan Wang
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern, University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yane Yang
- Shenzhen Far East Women & Children Hospital, Shenzhen, 518000, Guangdong, China
| | - Ping Li
- Shenzhen Far East Women & Children Hospital, Shenzhen, 518000, Guangdong, China
| | - Zhipeng Zeng
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wenlong Hu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Yumei Chen
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China.
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, ShenzhenPeople's Hospital, Shenzhen, Guangdong, 518020, People's Republic of China.
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Tan R, Li D, Hu N, Qiu J, Zeng Z, Cai W, Zhong Y, Zhang X, Pai P, Wang K, Tang D, Dai Y. Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease. Proteome Sci 2023; 21:18. [PMID: 37833721 PMCID: PMC10571336 DOI: 10.1186/s12953-023-00211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/16/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND End-stage renal disease (ESRD) is a condition that is characterized by the loss of kidney function. ESRD patients suffer from various endothelial dysfunctions, inflammation, and immune system defects. Lysine malonylation (Kmal) is a recently discovered post-translational modification (PTM). Although Kmal has the ability to regulate a wide range of biological processes in various organisms, its specific role in ESRD is limited. METHODS In this study, the affinity enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques have been used to create the first global proteome and malonyl proteome (malonylome) profiles of peripheral blood mononuclear cells (PBMCs) from twenty patients with ESRD and eighty-one controls. RESULTS On analysis, 793 differentially expressed proteins (DEPs) and 12 differentially malonylated proteins (DMPs) with 16 Kmal sites were identified. The Rap1 signaling pathway and platelet activation pathway were found to be important in the development of chronic kidney disease (CKD), as were DMPs TLN1 and ACTB, as well as one malonylated site. One conserved Kmal motif was also discovered. CONCLUSIONS These findings provided the first report on the Kmal profile in ESRD, which could be useful in understanding the potential role of lysine malonylation modification in the development of ESRD.
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Affiliation(s)
- Ruqi Tan
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China
- Department of Nephrology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, 518053, Guangdong, China
| | - Dandan Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China
- Experimental Center, Shenzhen Pingle Orthopedic Hospital (Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, Guangdong, 518118, China
| | - Nan Hu
- Key Renal Laboratory of Shenzhen, Department of Nephrology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Jing Qiu
- Key Renal Laboratory of Shenzhen, Department of Nephrology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China
| | - Wanxia Cai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China
| | - Yafang Zhong
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China
| | - Xinzhou Zhang
- Key Renal Laboratory of Shenzhen, Department of Nephrology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Pearl Pai
- Department of Nephrology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, 518053, Guangdong, China
| | - Kang Wang
- Key Renal Laboratory of Shenzhen, Department of Nephrology, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China.
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China.
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, P.R. China.
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, 232001, China.
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8
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Zheng Y, Zhu L, Qin ZY, Guo Y, Wang S, Xue M, Shen KY, Hu BY, Wang XF, Wang CQ, Qin LX, Dong QZ. Modulation of cellular metabolism by protein crotonylation regulates pancreatic cancer progression. Cell Rep 2023; 42:112666. [PMID: 37347667 DOI: 10.1016/j.celrep.2023.112666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
Protein lysine crotonylation has been recently identified as a vital posttranslational modification in cellular processes, particularly through the modification of histones. We show that lysine crotonylation is an important modification of the cytoplastic and mitochondria proteins. Enzymes in glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid metabolism, glutamine metabolism, glutathione metabolism, the urea cycle, one-carbon metabolism, and mitochondrial fusion/fission dynamics are found to be extensively crotonylated in pancreatic cancer cells. This modulation is mainly controlled by a pair of crotonylation writers and erasers including CBP/p300, HDAC1, and HDAC3. The dynamic crotonylation of metabolic enzymes is involved in metabolism regulation, which is linked with tumor progression. Interestingly, the activation of MTHFD1 by decrotonylation at Lys354 and Lys553 promotes the development of pancreatic cancer by increasing resistance to ferroptosis. Our study suggests that crotonylation represents a metabolic regulatory mechanism in pancreatic cancer progression.
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Affiliation(s)
- Yan Zheng
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Le Zhu
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China; Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, China
| | - Zhao-Yu Qin
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Yu Guo
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Shun Wang
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Min Xue
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Ke-Yu Shen
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Bei-Yuan Hu
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Xu-Feng Wang
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Chao-Qun Wang
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China
| | - Lun-Xiu Qin
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China.
| | - Qiong-Zhu Dong
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China; Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, China.
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9
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Quantitative Crotonylome Analysis Reveals the Mechanism of Shenkang Injection on Diabetic Nephropathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022. [DOI: 10.1155/2022/7767431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shenkang injection (SKI) has been widely used in the clinical treatment of chronic kidney diseases in China because of its efficacy and safety. However, the underlying mechanism of SKI in diabetic nephropathy (DN) remains unclear. The present study aimed to investigate the renoprotective effects and possible mechanisms of SKI in diabetic db/db mice. We showed that SKI ameliorated hyperglycemia and abnormal renal biochemical parameters in db/db mice. Crotonylome and subsequent bioinformatics analyses indicated that the molecular functions of the significantly different crotonylated proteins regulated by SKI were closely related to oxidoreductase activity and oxidative phosphorylation might be one of the main pathways through which SKI functions in DN. Subsequent PRM validation of the selected crotonylated proteins confirmed these findings. In addition, we determined that SKI could regulate the expression of specific proteins in oxidative phosphorylation complexes and enhance antioxidant capacity. Taken together, our data suggest that SKI exerted the protective effect against DN potentially through reversing the abnormal crotonylation expression of oxidoreductase-related proteins.
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10
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Cao SH, Chen ZH, Ma RY, Yue L, Jiang HM, Dong LH. Dynamics and Functional Interplay of Nonhistone Lysine Crotonylome and Ubiquitylome in Vascular Smooth Muscle Cell Phenotypic Remodeling. Front Cardiovasc Med 2022; 9:783739. [PMID: 35369347 PMCID: PMC8964401 DOI: 10.3389/fcvm.2022.783739] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe crotonylation of histones is discovered of late as one of the post-translational modifications (PTMs) that can regulate gene expression. However, the function of crotonylation on nonhistone proteins in vascular smooth muscle cells (VSMCs) is unclear. Here, we aim to find the cellular characteristics of crotonylated nonhistone proteins and the cross talk with ubiquitinated proteins in VSMC phenotypic remodeling using the modified omics and proteomic analysis.MethodsWe performed the modified omics and proteomic analysis of VSMCs before and after the stimulation with platelet-derived growth factor-BB (PDGF-BB). The crotonylated and ubiquitinated pan-antibody was used to enrich proteins and then subjected to a high-throughput mass spectrometry analysis. The enrichment analysis was performed within differentially modified proteins in regard to GO terms, KEGG, and protein domains.ResultsAs a result, there were 2,138 crotonylation sites in 534 proteins and 1,359 ubiquitination sites corresponding to 657 proteins. These crotonylated proteins detected after PDGF-BB stimulation might be involved in various vital cellular pathways and carry out important functions in VSMCs. Some of them closely took part in significant physiological processes of VSMC phenotypic remodeling, including glycolysis/gluconeogenesis, vascular smooth muscle contraction, and the PI3K-Akt signaling pathway. Furthermore, the KEGG pathway enrichment analysis showed the involvement of ubiquitinated proteins in the physiological processes of VSMC phenotypic remodeling, including glycolysis/gluconeogenesis, vascular smooth muscle contraction, RAS signaling pathway, or the PI3K-Akt signaling pathway. A cross talk analysis showed that there were 199 sites within the 177 proteins modified by crotonylation and ubiquitination simultaneously. Protein–protein interaction (PPI) network analysis indicated that crotonylated and ubiquitinated proteins play an important role in cellular bioprocess commonly and possibly have a synergistic effect.ConclusionIn summary, our bioinformatics analysis shows that the crotonylation and ubiquitination of nonhistone proteins play an essential role in VSMC phenotypic transformation induced by PDGF-BB stimulation. The cross talk between crotonylation and ubiquitination in glycolysis is possibly a novel mechanism during VSMC phenotypic remodeling.
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11
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Menter DG, Afshar-Kharghan V, Shen JP, Martch SL, Maitra A, Kopetz S, Honn KV, Sood AK. Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective. Cancer Metastasis Rev 2022; 41:147-172. [PMID: 35022962 PMCID: PMC8754476 DOI: 10.1007/s10555-022-10019-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/04/2022] [Indexed: 01/08/2023]
Abstract
We have established considerable expertise in studying the role of platelets in cancer biology. From this expertise, we were keen to recognize the numerous venous-, arterial-, microvascular-, and macrovascular thrombotic events and immunologic disorders are caused by severe, acute-respiratory-syndrome coronavirus 2 (SARS-CoV-2) infections. With this offering, we explore the evolutionary connections that place platelets at the center of hemostasis, immunity, and adaptive phylogeny. Coevolutionary changes have also occurred in vertebrate viruses and their vertebrate hosts that reflect their respective evolutionary interactions. As mammals adapted from aquatic to terrestrial life and the heavy blood loss associated with placentalization-based live birth, platelets evolved phylogenetically from thrombocytes toward higher megakaryocyte-blebbing-based production rates and the lack of nuclei. With no nuclei and robust RNA synthesis, this adaptation may have influenced viral replication to become less efficient after virus particles are engulfed. Human platelets express numerous receptors that bind viral particles, which developed from archetypal origins to initiate aggregation and exocytic-release of thrombo-, immuno-, angiogenic-, growth-, and repair-stimulatory granule contents. Whether by direct, evolutionary, selective pressure, or not, these responses may help to contain virus spread, attract immune cells for eradication, and stimulate angiogenesis, growth, and wound repair after viral damage. Because mammalian and marsupial platelets became smaller and more plate-like their biophysical properties improved in function, which facilitated distribution near vessel walls in fluid-shear fields. This adaptation increased the probability that platelets could then interact with and engulf shedding virus particles. Platelets also generate circulating microvesicles that increase membrane surface-area encounters and mark viral targets. In order to match virus-production rates, billions of platelets are generated and turned over per day to continually provide active defenses and adaptation to suppress the spectrum of evolving threats like SARS-CoV-2.
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Affiliation(s)
- David G Menter
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Vahid Afshar-Kharghan
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John Paul Shen
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie L Martch
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth V Honn
- Department of Pathology, Bioactive Lipids Research Program, Wayne State University, 5101 Cass Ave. 430 Chemistry, Detroit, MI, 48202, USA
- Department of Pathology, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA
- Cancer Biology Division, Wayne State University School of Medicine, 431 Chemistry Bldg, Detroit, MI, 48202, USA
| | - Anil K Sood
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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12
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Wang S, Mu G, Qiu B, Wang M, Yu Z, Wang W, Wang J, Yang Y. The Function and related Diseases of Protein Crotonylation. Int J Biol Sci 2021; 17:3441-3455. [PMID: 34512158 PMCID: PMC8416722 DOI: 10.7150/ijbs.58872] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Crotonylation is a kind of newly discovered acylation modification. Thousands of crotonylation sites have been identified in histone and non-histone proteins over the past decade. As a modification closely related to acetylation, crotonylation was reported to share many universal enzymes with acetylation. Crotonylated proteins have important roles in the regulation of various biological processes, such as gene expression, process of spermatogenesis, cell cycle, and also in the pathogenesis of different diseases, which range from depression to cancer. In this review, we summarize the research processes of crotonylation and discuss the advances of regulation mechanism of both histone and non-histone proteins crotonylation in difference physiological processes. Also, we focus on the alteration of the crotonylation under certain pathological conditions and its role in the pathogenesis of each disease.
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Affiliation(s)
- Shuo Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guanqun Mu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bingquan Qiu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Meng Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zunbo Yu
- China Institute of Veterinary Drugs Control, Beijing 100181, China
| | - Weibin Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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13
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Zheng F, Xu H, Huang S, Zhang C, Li S, Wang K, Dai W, Zhang X, Tang D, Dai Y. The Landscape and Potential Regulatory Mechanism of Lysine 2-Hydroxyisobutyrylation of Protein in End-Stage Renal Disease. Nephron Clin Pract 2021; 145:760-769. [PMID: 34515164 DOI: 10.1159/000518424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/07/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acetylation has a vital role in the pathogenesis of end-stage renal disease (ESRD). Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of acetylation. In this study, we aimed to reveal the key features of Khib in peripheral blood monocytes (PBMCs) of patients with ESRD. METHOD We combined TMT labeling with LC-MS/MS analysis to compare Khib modification of PBMCs between 20 ESRD patients and 20 healthy controls. The pan 2-hydroxyisobutyrylation antibody-based affinity enrichment method was used to reveal the features of Khib, and the bioinformatics analysis was conducted to analyze the pathology of these Khib-modified proteins. RESULT Compared to healthy controls, we identified 440 upregulated proteins and 552 downregulated proteins in PBMCs of ESRD, among which 579 Khib sites on 324 upregulated proteins and 287 Khib sites on 188 downregulated proteins were identified. The site abundance, distribution, and function of the Khib protein were further analyzed. The bioinformatics analysis revealed that the Rho/ROCK signaling pathway was highly enriched in ESRD, suggesting that it might contribute to renal fibrosis in ESRD patients. CONCLUSION In this study, we found that Khib-modified proteins correlated with the occurrence and progression of ESRD.
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Affiliation(s)
- Fengping Zheng
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China, .,Department of Clinical Medical Research Center, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China,
| | - Huixuan Xu
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Shaoying Huang
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Cantong Zhang
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Shanshan Li
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Kang Wang
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Weier Dai
- College of Natural Science, the University of Texas at Austin, Austin, Texas, USA
| | - Xinzhou Zhang
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Donge Tang
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
| | - Yong Dai
- Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China.,Department of Clinical Medical Research Center, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen, China
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14
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Huang J, Tang D, Zheng F, Xu H, Dai Y. Comprehensive analysis of lysine crotonylation modification in patients with chronic renal failure. BMC Nephrol 2021; 22:310. [PMID: 34517817 PMCID: PMC8439085 DOI: 10.1186/s12882-021-02445-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Post-translational modifications (PTMs) are at the heart of many cellular signaling events, which changes the function of protein. Crotonylation, one of the most important and common PTMs, plays a crucial role in the regulation of various biological processes. However, no study has evaluated the role of lysine crotonylation modification in chronic renal failure (CRF) patients. METHODS Here, we comparatively evaluated the crotonylation proteome of normal controls and chronic renal failure patients using liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with highly sensitive immune-affinity purification. RESULTS A total of 1109 lysine modification sites were identified, of which 772 sites were up-regulated and 69 sites were down-regulated. This suggested that crotonylation modification maintains high levels in the patients with chronic renal failure. Gene ontology(GO) enrichment analysis showed that the crotonylated proteins were significantly enriched in the platelet alpha granule lumen, platelet degradulation, and cell adhesion molecule binding. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional enrichment analysis in the Kyoto encyclopedia showed that crotonylated protein was enriched in CD36, which is closely linked to renal failure. CONCLUSIONS This is the first report of the global crotonylation proteome in chronic renal failure patients. Crotonylation of histone and non-histone may play important roles in delaying the continuous deterioration of renal function in patients with chronic renal failure.
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Affiliation(s)
- Jiahuang Huang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease,, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital,, Guangdong, 518020, Shenzhen, P.R. China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease,, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital,, Guangdong, 518020, Shenzhen, P.R. China
| | - Fengping Zheng
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease,, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital,, Guangdong, 518020, Shenzhen, P.R. China
| | - Huixuan Xu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease,, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital,, Guangdong, 518020, Shenzhen, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease,, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital,, Guangdong, 518020, Shenzhen, P.R. China.
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15
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Kanikarla Marie P, Fowlkes NW, Afshar-Kharghan V, Martch SL, Sorokin A, Shen JP, Morris VK, Dasari A, You N, Sood AK, Overman MJ, Kopetz S, Menter DG. The Provocative Roles of Platelets in Liver Disease and Cancer. Front Oncol 2021; 11:643815. [PMID: 34367949 PMCID: PMC8335590 DOI: 10.3389/fonc.2021.643815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Both platelets and the liver play important roles in the processes of coagulation and innate immunity. Platelet responses at the site of an injury are rapid; their immediate activation and structural changes minimize the loss of blood. The majority of coagulation proteins are produced by the liver—a multifunctional organ that also plays a critical role in many processes: removal of toxins and metabolism of fats, proteins, carbohydrates, and drugs. Chronic inflammation, trauma, or other causes of irreversible damage to the liver can dysregulate these pathways leading to organ and systemic abnormalities. In some cases, platelet-to-lymphocyte ratios can also be a predictor of disease outcome. An example is cirrhosis, which increases the risk of bleeding and prothrombotic events followed by activation of platelets. Along with a triggered coagulation cascade, the platelets increase the risk of pro-thrombotic events and contribute to cancer progression and metastasis. This progression and the resulting tissue destruction is physiologically comparable to a persistent, chronic wound. Various cancers, including colorectal cancer, have been associated with increased thrombocytosis, platelet activation, platelet-storage granule release, and thrombosis; anti-platelet agents can reduce cancer risk and progression. However, in cancer patients with pre-existing liver disease who are undergoing chemotherapy, the risk of thrombotic events becomes challenging to manage due to their inherent risk for bleeding. Chemotherapy, also known to induce damage to the liver, further increases the frequency of thrombotic events. Depending on individual patient risks, these factors acting together can disrupt the fragile balance between pro- and anti-coagulant processes, heightening liver thrombogenesis, and possibly providing a niche for circulating tumor cells to adhere to—thus promoting both liver metastasis and cancer-cell survival following treatment (that is, with minimal residual disease in the liver).
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Affiliation(s)
- Preeti Kanikarla Marie
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalie W Fowlkes
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vahid Afshar-Kharghan
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephanie L Martch
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alexey Sorokin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - David George Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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16
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Jiang G, Li C, Lu M, Lu K, Li H. Protein lysine crotonylation: past, present, perspective. Cell Death Dis 2021; 12:703. [PMID: 34262024 PMCID: PMC8280118 DOI: 10.1038/s41419-021-03987-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 02/08/2023]
Abstract
Lysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.
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Affiliation(s)
- Gaoyue Jiang
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Chunxia Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Meng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China.
| | - Huihui Li
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China.
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17
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Xu M, Xie Y, Li Y, Shen L, Huang K, Lin Z, Li B, Xia C, Zhang X, Chi Y, Zhang B, Yang J. Proteomic Analysis of Histone Crotonylation Suggests Diverse Functions in Myzus persicae. ACS OMEGA 2021; 6:16391-16401. [PMID: 34235310 PMCID: PMC8246447 DOI: 10.1021/acsomega.1c01194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Myzus persicae is one of the most important economic pests of cultivated crops. In the present study, we used an integrated approach involving high-performance liquid chromatography fractionation, affinity enrichment, and mass spectrometry-based proteomics to carry out a comprehensive proteomic analysis of lysine crotonylation in M. persicae. Altogether, 7530 lysine crotonylation sites were identified in 2452 protein groups. Intensive bioinformatic analyses were then carried out to annotate those lysine crotonylated targets identified in terms of Gene Ontology annotation, domain annotation, subcellular localization, Kyoto Encyclopedia of Genes and Genomes pathway annotation, functional cluster analysis, etc. Analysis results showed that lysine-crotonylated proteins were involved in many biological processes, such as the amino acid metabolism, aminoacyl-tRNA biosynthesis, spliceosomes, ribosomes, and so forth. Notably, the interaction network showed that there were 199 crotonylated proteins involved in the amino acid metabolism and numerous crotonylation targets associated with fatty acid biosynthesis and degradation. The results provide a system-wide view of the entire M. persicae crotonylome and a rich data set for functional analysis of crotonylated proteins in this economically important pest, which marks an important beginning for the further research.
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Affiliation(s)
- Manlin Xu
- Tobacco
Research Institute of CAAS, Qingdao, Shandong 266101, China
- Shandong
Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Yi Xie
- Tobacco
Research Institute of CAAS, Qingdao, Shandong 266101, China
| | - Ying Li
- Tobacco
Research Institute of CAAS, Qingdao, Shandong 266101, China
| | - Lili Shen
- Tobacco
Research Institute of CAAS, Qingdao, Shandong 266101, China
| | - Kun Huang
- Tobacco
Company of Yunnan Province, Honghe Company, Mile, Yunnan 652300, China
| | - Zhonglong Lin
- China
Tobacco Corporation Yunnan Company, Kunming, Yunnan 650000, China
| | - Bin Li
- China
Tobacco Corporation Sichuan Company, Chengdu, Sichuan 610000, China
| | - Changjian Xia
- Haikou Cigar
Research Institute, Hainan Provincial Branch
of China National Tobacco Corporation (CNTC), Haikou, Hainan 570100, China
| | - Xia Zhang
- Shandong
Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Yucheng Chi
- Shandong
Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Bin Zhang
- Qingdao
Agricultural University, Qingdao, Shandong 266109, China
| | - Jinguang Yang
- Tobacco
Research Institute of CAAS, Qingdao, Shandong 266101, China
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18
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Dong J, Li Y, Zheng F, Chen W, Huang S, Zhou X, Wang K, Cai W, Liu H, Yin L, Li Q, Tang D, Dai Y. Co-occurrence of Protein Crotonylation and 2-Hydroxyisobutyrylation in the Proteome of End-Stage Renal Disease. ACS OMEGA 2021; 6:15782-15793. [PMID: 34179622 PMCID: PMC8223210 DOI: 10.1021/acsomega.1c01161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/25/2021] [Indexed: 05/16/2023]
Abstract
End-stage renal disease (ESRD) is gradually becoming a major public healthcare burden worldwide. Post-translational modifications carrying epigenetic information play a crucial role in the pathogenesis of many chronic diseases. We performed lysine crotonylation (KCr) and lysine 2-hydroxyisobutyrylation (Khib) analyses with liquid chromatography-tandem mass spectrometry to obtain a comprehensive profile and reveal the specific pathogenesis of peripheral blood mononuclear cells in ESRD patients. 218 overlap proteins among differentially modified proteins (DMPs) of both 2-hydroxyisobutyrylation and crotonylation were identified. KEGG analysis enriched pathways of protein processing in endoplasmic reticulum (ER) and glycolysis/gluconeogenesis which is closely related with cell apoptosis. In Bip, a master regulator in the ER, eight sites were identified as having both KCr and Khib modifications. Five differentially KCr modification sites and three differentially Khib-modified sites were detected between ESRD patients and normal controls. Besides Bip, other proteins (GRP94, CNX, CRT, PDIs, GlcII, ERP57, Bap31, Hsp70, and Hsp90) happened both KCr and Khib modifications. Nine DMPs having both KCr and Khib modifications were related to the glycolysis/gluconeogenesis pathway containing two key regulatory enzymes of hexokinase-1 and pyruvate kinase. The two most abundant dual modification proteins were ENO1 and PGK1 with 15 sites and 8 sites, respectively. Lysine residue K228 with both KCr and Khib modifications in ENO1 was on its surface and made it accessible for p300 mediating dynamic modifications. Overall, we hypothesize that KCr and Khib comodifications may influence the number of immunocytes and further induce immune senescence in ESRD patients through the glycolysis/gluconeogenesis pathway and protein processing in the ER process, which may be a potential therapeutic direction in the future.
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Affiliation(s)
- Jingjing Dong
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Yixi Li
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Fengping Zheng
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wenbiao Chen
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Shaoying Huang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Xianqing Zhou
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
| | - Kang Wang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wanxia Cai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - HaiPing Liu
- The
Second People’s Hospital of Lianping County, Heyuan517139, Guangdong , China
| | - Lianghong Yin
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Li
- Dongguan
Hospital of Guangzhou University of Traditional Chinese Medicine, Dongguan 523000, Guangdong, China
- . Phone: +86 0769 26385192
| | - Donge Tang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- . Phone: +86 0755 22942106
| | - Yong Dai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
- . Phone: +86 0755 22942780
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19
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Hou JY, Zhou L, Li JL, Wang DP, Cao JM. Emerging roles of non-histone protein crotonylation in biomedicine. Cell Biosci 2021; 11:101. [PMID: 34059135 PMCID: PMC8166067 DOI: 10.1186/s13578-021-00616-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.
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Affiliation(s)
- Jia-Yi Hou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.,Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Lan Zhou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - De-Ping Wang
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
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20
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Lv Y, Bu C, Meng J, Ward C, Volpe G, Hu J, Jiang M, Guo L, Chen J, Esteban MA, Bao X, Cheng Z. Global Profiling of the Lysine Crotonylome in Different Pluripotent States. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:80-93. [PMID: 33746086 PMCID: PMC8498919 DOI: 10.1016/j.gpb.2021.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/21/2020] [Accepted: 01/27/2021] [Indexed: 12/19/2022]
Abstract
Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography–tandem mass spectrometry (LC–MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states including ground, metastable, and primed states, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis, central carbon metabolism, and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-coenzyme A (crotonyl-CoA) through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.
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Affiliation(s)
- Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Jin Meng
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jieyi Hu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lin Guo
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China.
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21
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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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22
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Xu M, Luo J, Li Y, Shen L, Zhang X, Yu J, Guo Z, Wu J, Chi Y, Yang J. First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.). Proteomics 2021; 21:e2000156. [PMID: 33480167 DOI: 10.1002/pmic.202000156] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Lysine crotonylation is an important post-translational modification process. Most research in this area has been carried out on mammals and yeast, but there has been little research on it in plants. In the current study, large-scale lysine crotonylome analysis was performed by a combination of affinity enrichment and high-resolution LC-MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine-crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, biosynthesis of amino acids, ribosomes structure and function. In particular, subcellular localization analysis showed that 43% of the crotonylated proteins were located in the chloroplast. Twenty-nine crotonylation proteins were associated with photosynthesis and functional enrichment that these proteins were associated with the reaction center, photosynthetic electron transport, and ATP synthesis. Based on these results, further studies to expand on the lysine crotonylome analysis were suggested.
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Affiliation(s)
- Manlin Xu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jianda Luo
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Ying Li
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Lili Shen
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Juxiang Wu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Yucheng Chi
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jinguang Yang
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
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23
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Martinez-Moreno JM, Fontecha-Barriuso M, Martín-Sánchez D, Sánchez-Niño MD, Ruiz-Ortega M, Sanz AB, Ortiz A. The Contribution of Histone Crotonylation to Tissue Health and Disease: Focus on Kidney Health. Front Pharmacol 2020; 11:393. [PMID: 32308622 PMCID: PMC7145939 DOI: 10.3389/fphar.2020.00393] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Acute kidney injury (AKI) and chronic kidney disease (CKD) are the most severe consequences of kidney injury. They are interconnected syndromes as CKD predisposes to AKI and AKI may accelerate CKD progression. Despite their growing impact on the global burden of disease, there is no satisfactory treatment for AKI and current therapeutic approaches to CKD remain suboptimal. Recent research has focused on the therapeutic target potential of epigenetic regulation of gene expression, including non-coding RNAs and the covalent modifications of histones and DNA. Indeed, several drugs targeting histone modifications are in clinical use or undergoing clinical trials. Acyl-lysine histone modifications (e.g. methylation, acetylation, and crotonylation) have modulated experimental kidney injury. Most recently, increased histone lysine crotonylation (Kcr) was observed during experimental AKI and could be reproduced in cultured tubular cells exposed to inflammatory stress triggered by the cytokine TWEAK. The degree of kidney histone crotonylation was modulated by crotonate availability and crotonate supplementation protected from nephrotoxic AKI. We now review the functional relevance of histone crotonylation in kidney disease and other pathophysiological contexts, as well as the implications for the development of novel therapeutic approaches. These studies provide insights into the overall role of histone crotonylation in health and disease.
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Affiliation(s)
- Julio M Martinez-Moreno
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain
| | - Miguel Fontecha-Barriuso
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain
| | - Diego Martín-Sánchez
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain
| | - Maria D Sánchez-Niño
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain
| | - Marta Ruiz-Ortega
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain.,School of Medicine, Autonomous University of Madrid (UAM), Madrid, Spain
| | - Ana B Sanz
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain
| | - Alberto Ortiz
- Research Institute-Fundacion Jimenez Diaz, Autonomous University of Madrid (UAM), Madrid, Spain.,Red de Investigación Renal (REDinREN), Madrid, Spain.,School of Medicine, Autonomous University of Madrid (UAM), Madrid, Spain.,IRSIN, Madrid, Spain
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24
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Wan J, Liu H, Chu J, Zhang H. Functions and mechanisms of lysine crotonylation. J Cell Mol Med 2019; 23:7163-7169. [PMID: 31475443 PMCID: PMC6815811 DOI: 10.1111/jcmm.14650] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/16/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Lysine crotonylation is a newly discovered post‐translational modification, which is structurally and functionally different from the widely studied lysine acetylation. Recent advances in the identification and quantification of lysine crotonylation by mass spectrometry have revealed that non‐histone proteins are frequently crotonylated, implicating it in many biological processes through the regulation of chromatin remodelling, metabolism, cell cycle and cellular organization. In this review, we summarize the writers, erasers and readers of lysine crotonylation, and their physiological functions, including gene transcription, acute kidney injury, spermatogenesis, depression, telomere maintenance, HIV latency and cancer process. These findings not only point to the new functions for lysine crotonylation, but also highlight the mechanisms by which crotonylation regulates various cellular processes.
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Affiliation(s)
- Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Chu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongquan Zhang
- Department of Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
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25
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Differential occurrence of lysine 2-hydroxyisobutyrylation in psoriasis skin lesions. J Proteomics 2019; 205:103420. [DOI: 10.1016/j.jprot.2019.103420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022]
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