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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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Chen L, Huang L, Gu Y, Li C, Sun P, Xiang Y. Novel post-translational modifications of protein by metabolites with immune responses and immune-related molecules in cancer immunotherapy. Int J Biol Macromol 2024:133883. [PMID: 39033895 DOI: 10.1016/j.ijbiomac.2024.133883] [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: 07/01/2023] [Revised: 06/30/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
Tumour immunotherapy is an effective and essential treatment for cancer. However, the heterogeneity of tumours and the complex and changeable tumour immune microenvironment (TME) creates many uncertainties in the clinical application of immunotherapy, such as different responses to tumour immunotherapy and significant differences in individual efficacy. It makes anti-tumour immunotherapy face many challenges. Immunometabolism is a critical determinant of immune cell response to specific immune effector molecules, significantly affecting the effects of tumour immunotherapy. It is attributed mainly to the fact that metabolites can regulate the function of immune cells and immune-related molecules through the protein post-translational modifications (PTMs) pathway. This study systematically summarizes a variety of novel protein PTMs including acetylation, propionylation, butyrylation, succinylation, crotonylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, benzoylation, lactylation and isonicotinylation in the field of tumour immune regulation and immunotherapy. In particular, we elaborate on how different PTMs in the TME can affect the function of immune cells and lead to immune evasion in cancer. Lastly, we highlight the potential treatment with the combined application of target-inhibited protein modification and immune checkpoint inhibitors (ICIs) for improved immunotherapeutic outcomes.
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Affiliation(s)
- Lihua Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Lixiang Huang
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China
| | - Yu Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Chen Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Pengming Sun
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China.
| | - Yang Xiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China.
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3
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Cao D, Sun W, Li X, Jian L, Zhou X, Bode AM, Luo X. The role of novel protein acylations in cancer. Eur J Pharmacol 2024:176841. [PMID: 39033839 DOI: 10.1016/j.ejphar.2024.176841] [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: 03/04/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024]
Abstract
Novel protein acylations are a class of protein post-translational modifications, such as lactylation, succinylation, crotonylation, palmitoylation, and β-hydroxybutyrylation. These acylation modifications are common in prokaryotes and eukaryotes and play pivotal roles in various key cellular processes by regulating gene transcription, protein subcellular localization, stability and activity, protein-protein interactions, and protein-DNA interactions. The diversified acylations are closely associated with various human diseases, especially cancer. In this review, we provide an overview of the distinctive characteristics, effects, and regulatory factors of novel protein acylations. We also explore the various mechanisms through which novel protein acylations are involved in the occurrence and progression of cancer. Furthermore, we discuss the development of anti-cancer drugs targeting novel acylations, offering promising avenues for cancer treatment.
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Affiliation(s)
- Dan Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Wenxuan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Xinyi Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Lian Jian
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Xinran Zhou
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan 410078, PR China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, China; Molecular Imaging Research Center of Central South University, Changsha, Hunan 410078, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410078, China.
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4
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Chen X, Wang S, Chen K, Han Q. The global landscapes of lysine crotonylation in pseudorabies virus infection. Virology 2024; 598:110172. [PMID: 39018683 DOI: 10.1016/j.virol.2024.110172] [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: 04/20/2024] [Revised: 06/11/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Lysine crotonylation is a common occurrence in eukaryotic cells, regulating various physiological functions, including chromatin remodeling, cellular growth, and development. However, its involvement in viral infections has rarely been documented. In this study, we reveal that pseudorabies virus (PRV) infection significantly alters the global lysine crotonylation levels in porcine kidney PK-15 cells. Specifically, we identified a few viral proteins, including UL54, gM, gD, UL19, UL37, and UL46, which undergo crotonylation modification. Our observations indicate that at 20 h post-infection (hpi), 551 crotonylation sites were reduced across 345 proteins, while 47 new sites emerged in 37 proteins compared to the control group. By 40 hpi, 263 sites had decreased in 190 proteins, while 389 new sites appeared in 240 proteins. Deeper analysis revealed that the proteins with altered crotonylation levels were primarily involved in binding, catalytic activity, biosynthetic processes, ribosome activity, and metabolic processes. Additionally, our findings underscored the significance of ribosomes and the endoplasmic reticulum (ER), which were enriched with proteins exhibiting altered crotonylation. Overall, our study for the first time offers new insights into the relationship between crotonylation and herpes virus infection, paving the way for future investigations into the role of crotonylation in viral infections.
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Affiliation(s)
- Xiaoyong Chen
- Xingzhi College, Zhejiang Normal University, Jinhua, Zhejiang, PR China.
| | - Shuaiwei Wang
- Wenzhou Vocational College of Technology and Science, Wenzhou, Zhejiang, PR China
| | - Keyuan Chen
- Union Hospital, Fujian Medical University, Fuzhou, Fujian, PR China
| | - Qingsong Han
- Wenzhou Vocational College of Technology and Science, Wenzhou, Zhejiang, PR China
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Gao J, Zhao Y, Chen C, Ning Q. MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites. Anal Biochem 2024; 687:115426. [PMID: 38141798 DOI: 10.1016/j.ab.2023.115426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Crotonylation on lysine sites in human non-histone proteins plays a crucial role in biology activities. However, because traditional experimental methods for crotonylation site identification are time-consuming and labor-intensive, computational prediction methods have become increasingly popular in recent years. Despite its significance, crotonylation site prediction has received less attention in non-histone proteins than in histones. In this study, we proposed a Multi-View Neural Network for identification of Human Non-Histone Crotonylation sites, named MVNN-HNHC. MVNN-HNHC integrated multi-view encoding features and adaptive encoding features through multi-channel neural network to deeply learn about attribute differences between crotonylation sites and non-crotonylation sites from various aspects. In MVNN-HNHC, convolutional neural networks can obtain local information from these features, and bidirectional long short term memory networks were utilized to extract sequence information. Then, we employ the attention mechanism to fuse the outputs of various feature extraction modules. Finally, the fully connection network acted as the classifier to predict whether a lysine site was crotonylation site or non-crotonylation site. Performance metrics on independent test set, including sensitivity, specificity, accuracy, Matthews correlation coefficient, and area under the curve (AUC) values reach 80.06 %, 75.77 %, 77.06 %, 0.5203, and 0.7792, respectively. To verify the effectiveness of this method, we carry out a series of experiments and the results show that MVNN-HNHC is an effective tool for predicting crotonylation sites in non-histone proteins. The data and code are available on https://github.com/xbbxhbc/junjun0612.git.
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Affiliation(s)
- Jun Gao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yaomiao Zhao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Chen Chen
- Naval Architecture and Ocean Engineering College, Dalian Maritime University, Dalian, 116026, China.
| | - Qiao Ning
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, 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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Zheng J, Liu Y, Wei K, Shi J, Li L, Jiang X, Tao L. Identification of Crotonylation Metabolism Signature Predicting Overall Survival for Clear Cell Renal Cell Carcinoma. Int J Clin Pract 2023; 2023:5558034. [PMID: 38058677 PMCID: PMC10697778 DOI: 10.1155/2023/5558034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Background Immunotherapy shows promise in treating cancer by leveraging the immune system to combat cancer cells. However, the influence of crotonylation metabolism on the prognosis and tumor environment in ccRCC patients is not fully understood. Methods We conducted various systematic analyses, including prognosis and cluster analyses, to investigate the role of KAT2A in immunotherapy. We used qRT-PCR to compare KAT2A expression in cancer and adjacent tissues and among different cell lines. Additionally, we employed Cell Counting Kit-8, wound healing, and Transwell chamber assays to assess changes in the proliferative and metastatic ability of A498 and 786-O cells. Results We identified three clusters related to crotonylation metabolism, each with distinct prognosis and immune characteristics in ccRCC. We categorized CT1 as immune-inflamed, CT2 as immune-excluded, and CR3 as immune-desert. A new system, CRS, emerged as an effective predictor of patient outcomes with differing immune characteristics. Moreover, qRT-PCR revealed elevated KAT2A levels in ccRCC tissues and cell lines. KAT2A was found to promote ccRCC and correlate significantly with immunosuppressive elements and checkpoints. Reducing KAT2A expression hindered ccRCC cell growth and metastasis. Conclusion Our study highlights the critical role of crotonylation metabolism in cancer development and progression, particularly its link to poor prognosis. CRS proves to be an accurate predictor of patient outcomes and immune features in ccRCC. KAT2A shows strong associations with clinical factors and the immunosuppressive environment, suggesting potential for innovative immunotherapies in ccRCC treatment.
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Affiliation(s)
- Jie Zheng
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Yingqing Liu
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Kai Wei
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Jiewu Shi
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Lin Li
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Xuefeng Jiang
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Lingsong Tao
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
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Ji P, Zhang G, Guo Y, Song H, Yuan X, Hu X, Guo Z, Xia P, Shen R, Wang D. Protein crotonylation: An emerging regulator in DNA damage response. Life Sci 2023; 331:122059. [PMID: 37652154 DOI: 10.1016/j.lfs.2023.122059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DNA damage caused by internal or external factors lead to increased genomic instability and various diseases. The DNA damage response (DDR) is a crucial mechanism that maintaining genomic stability through detecting and repairing DNA damage timely. Post-translational modifications (PTMs) play significant roles in regulation of DDR. Among the present PTMs, crotonylation has emerged as a novel identified modification that is involved in a wide range of biological processes including gene expression, spermatogenesis, cell cycle, and the development of diverse diseases. In the past decade, numerous crotonylation sites have been identified in histone and non-histone proteins, leading to a more comprehensive and deep understanding of the function and mechanisms in protein crotonylation. This review provides a comprehensive overview of the regulatory mechanisms of protein crotonylation and the effect of crotonylation in DDR. Furthermore, the effect of protein crotonylation in tumor development and progression is presented, to inspire and explore the novel strategies for tumor therapy.
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Affiliation(s)
- Pengfei Ji
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Guokun Zhang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Yanan Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Haoyun Song
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xinyi Yuan
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xiaohui Hu
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Zhao Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Peng Xia
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Rong Shen
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Degui Wang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China; NHC Key Laboratory of diagnosis and therapy of Gastrointestinal Tumor, Lanzhou, Gansu Province 730000, China.
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Yang P, Qin Y, Zeng L, He Y, Xie Y, Cheng X, Huang W, Cao L. Crotonylation and disease: Current progress and future perspectives. Biomed Pharmacother 2023; 165:115108. [PMID: 37392654 DOI: 10.1016/j.biopha.2023.115108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Histone lysine crotonylation 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 histone and nonhistone crotonylation in reproduction, development, and disease. Although the regulatory enzyme systems and targets of crotonylation partially overlap with those of acetylation, the peculiar CC bond structure of crotonylation suggests that crotonylation may have specific biological functions. In this review, we summarize the latest research progress regarding crotonylation, especially its regulatory factors and relationship with diseases, which suggest further research directions for crotonylation and provide new ideas for developing disease intervention and treatment regimens.
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Affiliation(s)
- Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yuanyuan Qin
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Lisha Zeng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China
| | - Yanqiu He
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yumei Xie
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Xi Cheng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China.
| | - Ling Cao
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China.
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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11
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Zhang J, Shi G, Pang J, Zhu X, Feng Q, Na J, Ma W, Liu D, Songyang Z. Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch. Stem Cell Res Ther 2023; 14:63. [PMID: 37013624 PMCID: PMC10071711 DOI: 10.1186/s13287-023-03290-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: 06/30/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Post-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs). METHODS We investigated the role of crotonylation in hESC differentiation by introduce crotonate into the culture medium of GFP tagged LTR7 primed H9 cell and extended pluripotent stem cell lines. RNA-seq assay was used to determine the hESC transcriptional features. Through morphological changes, qPCR of pluripotent and germ layer-specific gene markers and flow cytometry analysis, we determined that the induced crotonylation resulted in hESC differentiating into the endodermal lineage. We performed targeted metabolomic analysis and seahorse metabolic measurement to investigate the metabolism features after crotonate induction. Then high-resolution tandem mass spectrometry (LC-MS/MS) revealed the target proteins in hESCs. In addition, the role of crotonylated glycolytic enzymes (GAPDH and ENOA) was evaluated by in vitro crotonylation and enzymatic activity assays. Finally, we used knocked-down hESCs by shRNA, wild GAPDH and GAPDH mutants to explore potential role of GAPDH crotonylation in regulating human embryonic stem cell differentiation and metabolic switch. RESULT We found that induced crotonylation in hESCs resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. Increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Large-scale crotonylation profiling of non-histone proteins revealed that metabolic enzymes were major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs. CONCLUSIONS Crotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis during endodermal differentiation from hESCs.
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Affiliation(s)
- Jingran Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xing Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingcai Feng
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jie Na
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
- Bioland Laboratory, Guangzhou, 510320, China.
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12
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Development and Validation of a Prognostic Signature Based on the Lysine Crotonylation Regulators in Head and Neck Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4444869. [PMID: 36814797 PMCID: PMC9940974 DOI: 10.1155/2023/4444869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 02/16/2023]
Abstract
Background Lysine crotonylation (Kcr) is a newly identified posttranslational modification type regulated by various enzymes and coenzymes, including lysine crotonyltransferase, lysine decrotonylase, and binding proteins. However, the role of Kcr regulators in head and neck squamous cell carcinoma (HNSCC) remains unknown. The aim of this study was to establish and validate a Kcr-related prognostic signature of HNSCC and to assess the clinical predictive value of this signature. Methods The mRNA expression profiles and clinicopathological data from The Cancer Genome Atlas (TCGA) database were downloaded to explore the clinical significance and prognostic value of these regulators in HNSCC. The least absolute shrinkage and selection operator (LASSO) Cox regression model was used to generate the Kcr-related prognostic signature for HNSCC. Subsequently, the GSE65858 dataset from the Gene Expression Omnibus (GEO) database was used to validate the signature. The prognostic value of the signature was evaluated using the Kaplan-Meier survival, receiver operating characteristic (ROC) curve, and univariate and multivariate Cox regression analyses. Results We established a nine-gene risk signature associated with the prognosis of HNSCC based on Kcr regulators. High-risk patients demonstrated significantly poorer overall survival (OS) than low-risk patients in the training (TCGA) and validation (GEO) datasets. Then, the time-dependent receiver operating characteristic (ROC) curve analysis showed that the nine-gene risk signature was more accurate for predicting the 5-year OS than other clinical parameters, including age, gender, T stage, N stage, and histologic grade in the TCGA and GEO datasets. Moreover, the Cox regression analysis showed that the constructed risk signature was an independent risk factor for HNSCC. Conclusion Our study identified and validated a nine-gene signature for HNSCC based on Kcr regulators. These results might contribute to prognosis stratification and treatment escalation for HNSCC patients.
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13
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Khanal J, Kandel J, Tayara H, Chong KT. CapsNh-Kcr: Capsule network-based prediction of lysine crotonylation sites in human non-histone proteins. Comput Struct Biotechnol J 2022; 21:120-127. [PMID: 36544479 PMCID: PMC9735261 DOI: 10.1016/j.csbj.2022.11.056] [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: 07/20/2022] [Revised: 11/10/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
Lysine crotonylation (Kcr) is one of the most important post-translational modifications (PTMs) that is widely detected in both histone and non-histone proteins. In fact, Kcr is reported to be involved in various biological processes, such as metabolism and cell differentiation. However, the available experimental methods for Kcr site identification are laborious and costly. To effectively replace existing experimental approaches, some computational methods have been developed in the last few years. The available computational methods still lack some important aspects, as they can only identify Kcr sites on either histone-only or combined histone and nonhistone proteins. Although a tool was developed to identify Kcr sites on non-histone proteins only, its performance is inadequate and the exploration of hidden Kcr patterns (motifs) has been completely ignored, which might be significant for detailed Kcr studies. Therefore, algorithms that can more effectively predict Kcr sites on non-histone proteins with their biological meaning need to be designed. Accordingly, we developed a novel deep learning (capsule network)-based model, named CapsNh-Kcr, for Kcr site prediction, particularly focusing on non-histone proteins. Based on the independent results, the proposed model achieves an AUC of 0.9120, which is approximately 6% higher than that of previous nhKcr model in the prediction of Kcr sites on non-histone proteins. Further, we revealed, for the first time, that the proposed model can represent obvious motif distribution across Kcr sites in non-histone proteins. The source code (in Python) is publicly available at https://github.com/Jhabindra-bioinfo/CapsNh-Kcr.
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Affiliation(s)
- Jhabindra Khanal
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Jeevan Kandel
- Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea,Corresponding authors at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (H. Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea (K.T. Chong).
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea,Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea,Corresponding authors at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (H. Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea (K.T. Chong).
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14
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Xie T, Dong J, Zhou X, Tang D, Li D, Chen J, Chen Y, Xu H, Xue W, Liu D, Hong X, Tang F, Yin L, Dai Y. Proteomics analysis of lysine crotonylation and 2-hydroxyisobutyrylation reveals significant features of systemic lupus erythematosus. Clin Rheumatol 2022; 41:3851-3858. [PMID: 35941338 PMCID: PMC9652266 DOI: 10.1007/s10067-022-06254-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/14/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
INTRODUCTION/OBJECTIVES To seek significant features of systemic lupus erythematosus (SLE) by utilizing bioinformatics analysis. METHOD Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify lysine crotonylation (Kcr) and lysine 2-hydroxyisobutyrylation (Khib) in peripheral blood mononuclear cells (PBMCs) of systemic lupus erythematosus (SLE) patients and normal controls. RESULTS Seventy-six differentially modified proteins (DMPs) dually modified by Kcr and Khib were identified between SLE patients and healthy people. GO enrichment analysis prompted significant enrichment of seventy-six DMPs in MHC class II protein complex binding and leukocyte migration. KEGG pathways were enriched in antigen processing and presentation pathway and leukocyte transendothelial migration pathway. Six DMPs (CLTC, HSPA1B, HSPA8, HSP90AB1, HSPD1, and PDIA3) were identified in antigen processing and presentation pathway, of which HSPA8 was the core protein. Significant changes of Kcr and Khib in HSPA8 may increase ATP hydrolysis and promote antigen binding to MHC II molecule. In leukocyte transendothelial migration pathway, 7 DMPs (ACTN1, ACTN4, EZR, MSN, RAC1, RHOA, and VCL) were identified. MSN was the protein with the most modification sites in this pathway. In amino terminal ferm region of MSN, Kcr and Khib expression change may lead to the adhesion between leukocytes and endothelial cells, which was an important step of leukocyte migration. CONCLUSION Kcr and Khib may promote the antigen presentation and jointly regulate the tissue damage mediated by leukocyte migration in SLE patients, which may play key roles in the pathogenesis of SLE probably. Key Points • Antigen processing and presentation and leukocyte transendothelial migration may play key roles in the pathogenesis of SLE.
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Affiliation(s)
- Ting Xie
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jingjing Dong
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, Guangdong, China
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Xianqing Zhou
- Department of Pathology, Guangxi Key Laboratory of Metabolic Diseases Research, No.924 Hospital of PLA Joint Logistic Support Force, Guilin, 541002, Guangxi, China
| | - Donge Tang
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Dandan Li
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jiejing Chen
- Department of Pathology, Guangxi Key Laboratory of Metabolic Diseases Research, No.924 Hospital of PLA Joint Logistic Support Force, Guilin, 541002, Guangxi, China
| | - Yumei Chen
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Huixuan Xu
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Wen Xue
- Department of Pathology, Guangxi Key Laboratory of Metabolic Diseases Research, No.924 Hospital of PLA Joint Logistic Support Force, Guilin, 541002, Guangxi, China
| | - Dongzhou Liu
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Xiaoping Hong
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Fang Tang
- Department of Pathology, Guangxi Key Laboratory of Metabolic Diseases Research, No.924 Hospital of PLA Joint Logistic Support Force, Guilin, 541002, Guangxi, China.
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Yong Dai
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China.
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15
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Chen LJ, Tu ZY, Wang Y, He YH, Wang X, Tao SZ, Xu YY, Li CR, Wang RL, Yang ZX, Sun J, Ma X, Zhang D. ATP5O Hypo-crotonylation Caused by HDAC2 Hyper-Phosphorylation Is a Primary Detrimental Factor for Downregulated Phospholipid Metabolism under Chronic Stress. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9834963. [PMID: 38645677 PMCID: PMC11030818 DOI: 10.34133/2022/9834963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 10/03/2022] [Indexed: 04/23/2024]
Abstract
Objective. Chronic stress (CS)-induced abnormal metabolism and other subsequent aspects of abnormality are threatening human health. Little is known regarding whether and how protein post-translational-modifications (PTMs) correlate with abnormal metabolism under CS. The aim of this study was to address this issue and also identify novel key protein PTM. Methods. First, we screened which pan-PTM had significant change between control and CS female mice and whether clinical CS females had similar pan-PTM change. Second, we performed quantitative PTM-omics and metabolomics to verify the correlation between abnormal protein PTMs and atypical metabolism. Third, we performed quantitative phospho-omics to identify the key PTM-regulating enzyme and investigate the interaction between PTM protein and PTM-regulating enzyme. Fourth, we attempted to rectify the abnormal metabolism by correcting the activity of the PTM-regulating enzyme. Finally, we examined whether the selected key protein was also correlated with stress scores and atypical metabolism in clinical women. Results. We initially found that multiple tissues of CS female mice have downregulated pan-crotonylation, and verified that the plasma of clinical CS females also had downregulated pan-crotonylation. Then we determined that ATP5O-K51 crotonylation decreased the most and also caused gross ATP5O decrement, whereas the plasma of CS mice had downregulated phospholipids. Next, downregulating ATP5O crotonylation partially recapitulated the downregulated phospholipid metabolism in CS mice. Next, we verified that HDAC2-S424 phosphorylation determined its decrotonylation activity on ATP5O-K51. Furthermore, correcting HDAC2 hyper-phosphorylation recovered the gross ATP5O level and partially rescued the downregulated phospholipid metabolism in CS mice. Finally, the ATP5O level was also significantly lower and correlated with high stress scores and downregulated phospholipid metabolism in clinical female plasma. Conclusion. This study discovered a novel PTM mechanism involving two distinct types of PTM in CS and provided a novel reference for the clinical precautions and treatments of CS.
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Affiliation(s)
- Liang-Jian Chen
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
- Department of Obstetrics and Gynecology,
Reproductive Medicine Center,
The First Affiliated Hospital of Anhui Medical University,
Hefei 230022,
China
| | - Zhi-Yuan Tu
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
- State Key Laboratory of Reproductive Medicine,
the Center for Clinical Reproductive Medicine,
The First Affiliated Hospital of Nanjing Medical University,
Nanjing,
210029,
China
| | - Yang Wang
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Yu-Hao He
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Xin Wang
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Shu-Zhen Tao
- State Key Laboratory of Reproductive Medicine,
the Center for Clinical Reproductive Medicine,
The First Affiliated Hospital of Nanjing Medical University,
Nanjing,
210029,
China
| | - Yang-Yang Xu
- State Key Laboratory of Reproductive Medicine,
the Center for Clinical Reproductive Medicine,
The First Affiliated Hospital of Nanjing Medical University,
Nanjing,
210029,
China
| | - Cong-Rong Li
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Ruo-Lei Wang
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Zhi-Xia Yang
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Jing Sun
- Department of Psychiatry,
Nanjing Brain Hospital affiliated to Nanjing Medical University,
Nanjing,
210029 Jiangsu,
China
| | - Xiang Ma
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
| | - Dong Zhang
- State Key Lab of Reproductive Medicine,
Nanjing Medical University,
Nanjing,
211166 Jiangsu,
China
- Animal Core Facility,
Nanjing Medical University,
Nanjing,
211166,
Jiangsu,
P .R.,
China
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16
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Zhou T, Cheng X, He Y, Xie Y, Xu F, Xu Y, Huang W. Function and mechanism of histone β-hydroxybutyrylation in health and disease. Front Immunol 2022; 13:981285. [PMID: 36172354 PMCID: PMC9511043 DOI: 10.3389/fimmu.2022.981285] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Histone post-translational modifications (HPTMs) are essential epigenetic mechanisms that affect chromatin-associated nuclear processes without altering the DNA sequence. With the application of mass spectrometry-based proteomics, novel histone lysine acylation, such as propionylation, butyrylation, crotonylation, malonylation, succinylation, glutarylation, and lactoylation have been successively discovered. The emerging diversity of the lysine acylation landscape prompted us to investigate the function and mechanism of these novel HPTMs in health and disease. Recently, it has been reported that β-hydroxybutyrate (BHB), the main component of the ketone body, has various protective roles beyond alternative fuel provision during starvation. Histone lysine β-hydroxybutyrylation (Kbhb) is a novel HPTMs identified by mass spectrometry, which regulates gene transcription in response to carbohydrate restriction or elevated BHB levels in vivo and vitro. Recent studies have shown that histone Kbhb is strongly associated with the pathogenesis of metabolic cardiovascular diseases, kidney diseases, tumors, neuropsychiatric disorders, and metabolic diseases suggesting it has different functions from histone acetylation and methylation. This review focuses on the writers, erasers, sites, and underlying functions of histone Kbhb, providing a glimpse into their complex regulation mechanism.
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Affiliation(s)
- Tingting Zhou
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Xi Cheng
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Yanqiu He
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Yumei Xie
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Fangyuan Xu
- Department of Rehabilitation, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yong Xu
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- *Correspondence: Wei Huang, ; Yong Xu,
| | - Wei Huang
- Department of Endocrinology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- Metabolism, Metabolic Vascular Diseases Key Laboratory of Sichuan Province, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- *Correspondence: Wei Huang, ; Yong Xu,
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17
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Song J, Ngo L, Bell K, Zheng YG. Chemoproteomic Profiling of Protein Substrates of a Major Lysine Acetyltransferase in the Native Cellular Context. ACS Chem Biol 2022; 17:1092-1102. [PMID: 35417122 DOI: 10.1021/acschembio.1c00935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The family of lysine acetyltransferases (KATs) regulates epigenetics and signaling pathways in eukaryotic cells. So far, knowledge of different KAT members contributing to the cellular acetylome is limited, which limits our understanding of biological functions of KATs in physiology and disease. Here, we found that a clickable acyl-CoA reporter, 3-azidopropanoyl CoA (3AZ-CoA), presented remarkable cell permeability and effectively acylated proteins in cells. We rationally engineered the major KAT member, histone acetyltransferase 1 (HAT1), to generate its mutant forms that displayed excellent bio-orthogonal activity for 3AZ-CoA in substrate labeling. We were able to apply the bio-orthogonal enzyme-cofactor pair combined with SILAC proteomics to achieve HAT1 substrate targeting, enrichment, and proteomic profiling in living cells. A total of 123 protein substrates of HAT1 were disclosed, underlining the multifactorial functions of this important enzyme than hitherto known. This study demonstrates the first example of utilizing bio-orthogonal reporters as a chemoproteomic strategy for substrate mapping of individual KAT isoforms in the native biological contexts.
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Affiliation(s)
- Jiabao Song
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Liza Ngo
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Kaylyn Bell
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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18
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Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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19
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Monte Neto RLD, Moreira POL, de Sousa AM, Garcia MADN, Maran SR, Moretti NS. Antileishmanial metallodrugs and the elucidation of new drug targets linked to post-translational modifications machinery: pitfalls and progress. Mem Inst Oswaldo Cruz 2022; 117:e210403. [PMID: 35320824 PMCID: PMC8944189 DOI: 10.1590/0074-02760220403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
Despite the increasing number of manuscripts describing potential alternative antileishmanial compounds, little is advancing on translating these knowledges to new products to treat leishmaniasis. This is in part due to the lack of standardisations during pre-clinical drug discovery stage and also depends on the alignment of goals among universities/research centers, government and pharmaceutical industry. Inspired or not by drug repurposing, metal-based antileishmanial drugs represent a class that deserves more attention on its use for leishmaniasis chemotherapy. Together with new chemical entities, progresses have been made on the knowledge of parasite-specific drug targets specially after using CRISPR/Cas system for functional studies. In this regard, Leishmania parasites undergoe post-translational modification as key regulators in several cellular processes, which represents an entire new field for drug target elucidation, once this is poorly explored. This perspective review describes the advances on antileishmanial metallodrugs and the elucidation of drug targets based on post-translational modifications, highlighting the limitations on the drug discovery/development process and suggesting standardisations focused on products addressed to who need it most.
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Affiliation(s)
- Rubens Lima do Monte Neto
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisas em Biotecnologia Aplicada ao Estudo de Patógenos, Belo Horizonte, MG, Brasil
| | - Paulo Otávio Lourenço Moreira
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisas em Biotecnologia Aplicada ao Estudo de Patógenos, Belo Horizonte, MG, Brasil
| | - Alessandra Mara de Sousa
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisas em Biotecnologia Aplicada ao Estudo de Patógenos, Belo Horizonte, MG, Brasil
| | - Miguel Antonio do Nascimento Garcia
- Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, Laboratório de Biologia Molecular de Patógenos, São Paulo, SP, Brasil
| | - Suellen Rodrigues Maran
- Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, Laboratório de Biologia Molecular de Patógenos, São Paulo, SP, Brasil
| | - Nilmar Silvio Moretti
- Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, Laboratório de Biologia Molecular de Patógenos, São Paulo, SP, Brasil
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20
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Zhang Y, Chen Y, Zhang Z, Tao X, Xu S, Zhang X, Zurashvili T, Lu Z, Bayascas JR, Jin L, Zhao J, Zhou X. Acox2 is a regulator of lysine crotonylation that mediates hepatic metabolic homeostasis in mice. Cell Death Dis 2022; 13:279. [PMID: 35351852 PMCID: PMC8964741 DOI: 10.1038/s41419-022-04725-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/22/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022]
Abstract
Acyl-CoA oxidase 2 (Acox2) is an enzyme involved in peroxisomal bile acid synthesis and branched-chain fatty acid degradation. Acox2 knockout (−/−) mice spontaneously developed liver cancer with marked lymphocytic infiltrate. Tandem-affinity purification coupled with mass spectrometry analysis revealed that Acox2 interacted with methylcrotonoyl-CoA carboxylase followed by co-immunoprecipitation confirmation. Here we reported that non-histone lysine crotonylation (Kcr) levels were downregulated in Acox2−/− mice livers. Interestingly, Kcr signals were concentrated in the nucleus of tumor cells but mostly located in the cytoplasm of adjacent normal liver cells of Acox2−/− mice. Quantitative analysis of the global crotonylome further revealed that 54% (27/50) of downregulated non-histone Kcr sites were located in mitochondrial (11/50) and peroxisomal (17/50) enzymes including Ehhadh, Scp2, Hsd17b4, Crot, Etfa, Cpt1a, Eci1/2, Hadha, Etfdh, and Idh2. Subsequent site-directed mutagenesis and transcriptome analysis revealed that Ehhadh K572cr might have site-specific regulatory roles by downregulating TOP3B expression that lead to increased DNA damage in vitro. Our findings suggested Acox2 is a regulator of Kcr that might play critical role on hepatic metabolic homeostasis.
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21
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Quantitative Proteomics Analysis Expands the Roles of Lysine β-Hydroxybutyrylation Pathway in Response to Environmental β-Hydroxybutyrate. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4592170. [PMID: 35251473 PMCID: PMC8894020 DOI: 10.1155/2022/4592170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 12/30/2022]
Abstract
Lysine β-hydroxybutyrylation (Kbhb) is a newly identified protein posttranslational modification (PTM) derived from β-hydroxybutyrate (BHB), a product of ketone body metabolism in liver. BHB could serve as an energy source and play a role in the suppression of oxidative stress. The plasma concentration of BHB could increase up to 20 mM during starvation and in pathological conditions. Despite the progress, how the cells derived from extrahepatic tissues respond to elevated environmental BHB remains largely unknown. Given that BHB can significantly drive Kbhb, we characterized the BHB-induced lysine β-hydroxybutyrylome and acetylome by quantitative proteomics. A total of 840 unique Kbhb sites on 429 proteins were identified, with 42 sites on 39 proteins increased by more than 50% in response to BHB. The results showed that the upregulated Kbhb induced by BHB was involved in aminoacyl-tRNA biosynthesis, 2-oxocarboxylic acid metabolism, citrate cycle, glycolysis/gluconeogenesis, and pyruvate metabolism pathways. Moreover, some BHB-induced Kbhb substrates were significantly involved in diseases such as cancer. Taken together, we investigate the dynamics of lysine β-hydroxybutyrylome and acetylome induced by environmental BHB, which reveals the roles of Kbhb in regulating various biological processes and expands the biological functions of BHB.
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22
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Qiao Y, Zhu X, Gong H. BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models. Bioinformatics 2022; 38:648-654. [PMID: 34643684 DOI: 10.1093/bioinformatics/btab712] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION As one of the most important post-translational modifications (PTMs), protein lysine crotonylation (Kcr) has attracted wide attention, which involves in important physiological activities, such as cell differentiation and metabolism. However, experimental methods are expensive and time-consuming for Kcr identification. Instead, computational methods can predict Kcr sites in silico with high efficiency and low cost. RESULTS In this study, we proposed a novel predictor, BERT-Kcr, for protein Kcr sites prediction, which was developed by using a transfer learning method with pre-trained bidirectional encoder representations from transformers (BERT) models. These models were originally used for natural language processing (NLP) tasks, such as sentence classification. Here, we transferred each amino acid into a word as the input information to the pre-trained BERT model. The features encoded by BERT were extracted and then fed to a BiLSTM network to build our final model. Compared with the models built by other machine learning and deep learning classifiers, BERT-Kcr achieved the best performance with AUROC of 0.983 for 10-fold cross validation. Further evaluation on the independent test set indicates that BERT-Kcr outperforms the state-of-the-art model Deep-Kcr with an improvement of about 5% for AUROC. The results of our experiment indicate that the direct use of sequence information and advanced pre-trained models of NLP could be an effective way for identifying PTM sites of proteins. AVAILABILITY AND IMPLEMENTATION The BERT-Kcr model is publicly available on http://zhulab.org.cn/BERT-Kcr_models/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yanhua Qiao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolei Zhu
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China
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23
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Monte Neto RLD, Moreira POL, de Sousa AM, Garcia MADN, Maran SR, Moretti NS. Antileishmanial metallodrugs and the elucidation of new drug targets linked to post-translational modifications machinery: pitfalls and progress. Mem Inst Oswaldo Cruz 2022. [DOI: 10.1590/0074-02760210403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Khanal J, Tayara H, Zou Q, To Chong K. DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network. Brief Bioinform 2021; 23:6457166. [PMID: 34882222 DOI: 10.1093/bib/bbab492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Lysine crotonylation (Kcr) is a posttranslational modification widely detected in histone and nonhistone proteins. It plays a vital role in human disease progression and various cellular processes, including cell cycle, cell organization, chromatin remodeling and a key mechanism to increase proteomic diversity. Thus, accurate information on such sites is beneficial for both drug development and basic research. Existing computational methods can be improved to more effectively identify Kcr sites in proteins. In this study, we proposed a deep learning model, DeepCap-Kcr, a capsule network (CapsNet) based on a convolutional neural network (CNN) and long short-term memory (LSTM) for robust prediction of Kcr sites on histone and nonhistone proteins (mammals). The proposed model outperformed the existing CNN architecture Deep-Kcr and other well-established tools in most cases and provided promising outcomes for practical use; in particular, the proposed model characterized the internal hierarchical representation as well as the important features from multiple levels of abstraction automatically learned from a small number of samples. The trained model was well generalized in other species (papaya). Moreover, we showed the features and properties generated by the internal capsule layer that can explore the internal data distribution related to biological significance (as a motif detector). The source code and data are freely available at https://github.com/Jhabindra-bioinfo/DeepCap-Kcr.
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Affiliation(s)
- Jhabindra Khanal
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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25
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Zheng C, Sun L. Qualitative lysine crotonylome analysis in the ovarian tissue of Harmonia axyridis (Pallas). PLoS One 2021; 16:e0258371. [PMID: 34662345 PMCID: PMC8523065 DOI: 10.1371/journal.pone.0258371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been studied at the proteomics level in a few species, with the study of Kcr in female fertility and in insect species is still lacking. Harmonia axyridis (Pallas) is a well-known beneficial insect used as a natural biological control agent against aphids in agriculture. Here, global Kcr identification in ovarian tissue of H. axyridis at diapause stage was performed to reveal potential roles for Kcr in H. axyridis ovarian cellular processes, female fertility and diapause regulation. In total, 3084 Kcr sites in 920 proteins were identified. Bioinformatic analyses revealed the distribution of these proteins in multiple subcellular localization categories and their involvement in diverse biological processes and metabolism pathways. Carbohydrate and energy metabolism related cellular processes including citric acid cycle, glycolysis and oxidative phosphorylation appeared be affected by Kcr modification. In addition, regulation of translation and protein biosynthesis may reflect Kcr involvement in diapause in H. axyridis, with Kcr affecting ribosome activities and amino acid metabolism. Moreover, Kcr modulation H. axyridis ovary development regulation may share some common mechanism with Kcr participation in some disease progression. These processes and pathways were uncovered under diapause stage, but possibly not enriched/specific for diapause stage due to limitations of qualitative proteomics experimental design. Our results informs on the potential for Kcr modifications to regulate female fertility and insect physiology.
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Affiliation(s)
- Changying Zheng
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
| | - Lijuan Sun
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
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26
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Subba P, Prasad TSK. Protein Crotonylation Expert Review: A New Lens to Take Post-Translational Modifications and Cell Biology to New Heights. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:617-625. [PMID: 34582706 DOI: 10.1089/omi.2021.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genome regulation, temporal and spatial variations in cell function, continues to puzzle and interest life scientists who aim to unravel the molecular basis of human health and disease, not to mention plant biology and ecosystem diversity. Despite important advances in epigenomics and protein post-translational modifications over the past decade, there is a need for new conceptual lenses to understand biological mechanisms that can help unravel the fundamental regulatory questions in genomes and the cell. To these ends, lys crotonylation (Kcr) is a reversible protein modification catalyzed by protein crotonyl transferases and decrotonylases. First identified on histones, Kcr regulates cellular processes at the chromatin level. Research thus far has revealed that Kcr marks promoter sites of active genes and potential enhancers. Eventually, Kcr on a number of nonhistone proteins was reported. The abundance of Kcr on ribosomal and myofilament proteins indicates its functional roles in protein synthesis and muscle contraction. Kcr has also been associated with pluripotency, spermiogenesis, and DNA repair. In plants, large-scale mass spectrometry-based experiments validated the roles of Kcr in photosynthesis. In this expert review, we present the latest thinking and findings on lys crotonylation with an eye to regulation of cell biology. We discuss the enrichment techniques, putative biological functions, and challenges associated with studying this protein modification with vast biological implications. Finally, we reflect on the future outlook about the broader relevance of Kcr in animals, microbes, and plant species.
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Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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27
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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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28
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Koronowski KB, Greco CM, Huang H, Kim JK, Fribourgh JL, Crosby P, Mathur L, Ren X, Partch CL, Jang C, Qiao F, Zhao Y, Sassone-Corsi P. Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation. Cell Rep 2021; 36:109487. [PMID: 34348140 PMCID: PMC8372761 DOI: 10.1016/j.celrep.2021.109487] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/03/2021] [Accepted: 07/14/2021] [Indexed: 01/20/2023] Open
Abstract
Ketone bodies are bioactive metabolites that function as energy substrates, signaling molecules, and regulators of histone modifications. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, and associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification, and one-carbon metabolic pathways. Kbhb inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, in parallel with altered metabolite levels. Our results illuminate the role of Kbhb in hepatic metabolism under ketogenic conditions and demonstrate a functional consequence of this modification on a central metabolic enzyme.
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Affiliation(s)
- Kevin B Koronowski
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Carolina M Greco
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - He Huang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jin-Kwang Kim
- Department of Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lavina Mathur
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cholsoon Jang
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Feng Qiao
- Department of Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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29
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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: 45] [Impact Index Per Article: 15.0] [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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30
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Chen Z, Zhao P, Li C, Li F, Xiang D, Chen YZ, Akutsu T, Daly RJ, Webb GI, Zhao Q, Kurgan L, Song J. iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization. Nucleic Acids Res 2021; 49:e60. [PMID: 33660783 PMCID: PMC8191785 DOI: 10.1093/nar/gkab122] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins. Rapid accumulation of sequences requires equally pervasive development of new predictive models, which depends on the availability of effective tools that support these efforts. We introduce iLearnPlus, the first machine-learning platform with graphical- and web-based interfaces for the construction of machine-learning pipelines for analysis and predictions using nucleic acid and protein sequences. iLearnPlus provides a comprehensive set of algorithms and automates sequence-based feature extraction and analysis, construction and deployment of models, assessment of predictive performance, statistical analysis, and data visualization; all without programming. iLearnPlus includes a wide range of feature sets which encode information from the input sequences and over twenty machine-learning algorithms that cover several deep-learning approaches, outnumbering the current solutions by a wide margin. Our solution caters to experienced bioinformaticians, given the broad range of options, and biologists with no programming background, given the point-and-click interface and easy-to-follow design process. We showcase iLearnPlus with two case studies concerning prediction of long noncoding RNAs (lncRNAs) from RNA transcripts and prediction of crotonylation sites in protein chains. iLearnPlus is an open-source platform available at https://github.com/Superzchen/iLearnPlus/ with the webserver at http://ilearnplus.erc.monash.edu/.
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Affiliation(s)
- Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Chen Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Fuyi Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.,Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Dongxu Xiang
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Yong-Zi Chen
- Laboratory of Tumor Cell Biology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Roger J Daly
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China.,Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
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31
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Huang Q, Liao X, Yang X, Luo Y, Lin P, Zeng Q, Bai H, Jiang B, Pan Y, Zhang F, Zhang L, Jia Y, Liu Q. Lysine crotonylation of DgTIL1 at K72 modulates cold tolerance by enhancing DgnsLTP stability in chrysanthemum. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1125-1140. [PMID: 33368971 PMCID: PMC8196654 DOI: 10.1111/pbi.13533] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 05/10/2023]
Abstract
Lysine crotonylation of proteins is a recently identified post-translational modification (PTM) in plants. However, the function of lysine-crotonylated proteins in response to abiotic stress in plants has not been reported. In this study, we identified a temperature-induced lipocalin-1-like gene (DgTIL1) from chrysanthemum and showed that it was notably induced in response to cold stress. Overexpression of DgTIL1 enhanced cold tolerance in transgenic chrysanthemum. Ubiquitin membrane yeast two-hybrid (MYTH) system and bimolecular fluorescence complementation (BIFC) assays showed that DgTIL1 interacts with a nonspecific lipid transfer protein (DgnsLTP), which can promote peroxidase (POD) gene expression and POD activity to reduce the accumulation of reactive oxygen species (ROS) and improve resistance to cold stress in DgnsLTP transgenic chrysanthemum. In addition, we found that DgTIL1 was lysine crotonylated at K72 in response to low temperature in chrysanthemum. Moreover, lysine crotonylation of DgTIL1 prevented DgnsLTP protein degradation in tobacco and chrysanthemum. Inhibition of DgnsLTP degradation by lysine crotonylation of DgTIL1 further enhanced POD expression and POD activity, reduced the accumulation of ROS under cold stress in DgTIL1 transgenic chrysanthemum, thus promoting the cold resistance of chrysanthemum.
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Affiliation(s)
- Qiuxiang Huang
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Xiaoqin Liao
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Xiaohan Yang
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Yunchen Luo
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Ping Lin
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Qinhan Zeng
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Huiru Bai
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Beibei Jiang
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Yuanzhi Pan
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Fan Zhang
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Lei Zhang
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Yin Jia
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- Department of Ornamental HorticultureSichuan Agricultural UniversityChengduChina
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32
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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: 3] [Impact Index Per Article: 1.0] [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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33
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Chen YZ, Wang ZZ, Wang Y, Ying G, Chen Z, Song J. nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Brief Bioinform 2021; 22:6277413. [PMID: 34002774 DOI: 10.1093/bib/bbab146] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identification of Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and expensive when compared with computational approaches. To date, several predictors for Kcr site prediction have been developed, most of which are capable of predicting crotonylation sites on either histones alone or mixed histone and nonhistone proteins together. These methods exhibit high diversity in their algorithms, encoding schemes, feature selection techniques and performance assessment strategies. However, none of them were designed for predicting Kcr sites on nonhistone proteins. Therefore, it is desirable to develop an effective predictor for identifying Kcr sites from the large amount of nonhistone sequence data. For this purpose, we first provide a comprehensive review on six methods for predicting crotonylation sites. Second, we develop a novel deep learning-based computational framework termed as CNNrgb for Kcr site prediction on nonhistone proteins by integrating different types of features. We benchmark its performance against multiple commonly used machine learning classifiers (including random forest, logitboost, naïve Bayes and logistic regression) by performing both 10-fold cross-validation and independent test. The results show that the proposed CNNrgb framework achieves the best performance with high computational efficiency on large datasets. Moreover, to facilitate users' efforts to investigate Kcr sites on human nonhistone proteins, we implement an online server called nhKcr and compare it with other existing tools to illustrate the utility and robustness of our method. The nhKcr web server and all the datasets utilized in this study are freely accessible at http://nhKcr.erc.monash.edu/.
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Affiliation(s)
- Yong-Zi Chen
- Laboratory of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | | | | | - Guoguang Ying
- Laboratory of Tumor Cell Biology in Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, China
| | - Jiangning Song
- Monash Biomedicine Discovery Institute, Monash University, Australia
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34
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Keenan EK, Zachman DK, Hirschey MD. Discovering the landscape of protein modifications. Mol Cell 2021; 81:1868-1878. [PMID: 33798408 DOI: 10.1016/j.molcel.2021.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/21/2021] [Accepted: 03/10/2021] [Indexed: 02/08/2023]
Abstract
Protein modifications modulate nearly every aspect of cell biology in organisms, ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20th century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass-spectrometry-based proteomics in the latter part of the 20th century enabled a veritable explosion in the number of known protein modifications, with more than 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress in discovering new protein modifications and determining their function. In this review, we take an opportunity to revisit the historical discovery of key post-translational modifications, quantify the current landscape of covalent protein adducts, and assess the role that new computational tools will play in the future of this field.
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Affiliation(s)
- E Keith Keenan
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Derek K Zachman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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35
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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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36
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Li FC, Nie LB, Elsheikha HM, Yin FY, Zhu XQ. Lysine crotonylation is widespread on proteins of diverse functions and localizations in Toxoplasma gondii. Parasitol Res 2021; 120:1617-1626. [PMID: 33655350 DOI: 10.1007/s00436-021-07057-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/17/2021] [Indexed: 12/27/2022]
Abstract
Lysine crotonylation (Kcr) is an evolutionally conserved post-translational modification (PTM) on histone proteins. However, information about Kcr and its involvement in the biology and metabolism of Toxoplasma gondii is limited. In the present study, a global Kcr proteome analysis using LC-MS/MS in combination with immune-affinity method was performed. A total of 12,152 Kcr sites distributed over 2719 crotonylated proteins were identified. Consistent with lysine acetylation and succinylation in Apicomplexa, Kcr was associated with various metabolic pathways, including carbon metabolism, pyrimidine metabolism, glycolysis, gluconeogenesis, and proteasome. Markedly, many stage-specific proteins, histones, and histone-modifying enzymes related to the stage transition were found to have Kcr sites, suggesting a potential involvement of Kcr in the parasite stage transformation. Most components of the apical secretory organelles were identified as crotonylated proteins which were associated with the attachment, invasion, and replication of T. gondii. These results expanded our understanding of Kcr proteome and proposed new hypotheses for further research of the Kcr roles in the pathobiology of T. gondii infection.
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Affiliation(s)
- Fa-Cai Li
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China
| | - Lan-Bi Nie
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Fang-Yuan Yin
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, People's Republic of China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi Province, People's Republic of China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
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37
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Huang H, Zhang D, Weng Y, Delaney K, Tang Z, Yan C, Qi S, Peng C, Cole PA, Roeder RG, Zhao Y. The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway. SCIENCE ADVANCES 2021; 7:7/9/eabe2771. [PMID: 33627428 PMCID: PMC7904266 DOI: 10.1126/sciadv.abe2771] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/12/2021] [Indexed: 05/07/2023]
Abstract
Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyrate to lysine (Kbhb), while histone deacetylase 1 (HDAC1) and HDAC2 enzymatically remove Kbhb. We demonstrate that p300-dependent histone Kbhb can directly mediate in vitro transcription. Moreover, a comprehensive analysis of Kbhb substrates in mammalian cells has identified 3248 Kbhb sites on 1397 substrate proteins. The dependence of histone Kbhb on p300 argues that enzyme-catalyzed acylation is the major mechanism for nuclear Kbhb. Our study thus reveals key regulatory elements for the Kbhb pathway, laying a foundation for studying its roles in diverse cellular processes.
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Affiliation(s)
- He Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yejing Weng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kyle Delaney
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Cong Yan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shankang Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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38
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p300-Catalyzed Lysine Crotonylation Promotes the Proliferation, Invasion, and Migration of HeLa Cells via Heterogeneous Nuclear Ribonucleoprotein A1. ACTA ACUST UNITED AC 2020; 2020:5632342. [PMID: 33457194 PMCID: PMC7787849 DOI: 10.1155/2020/5632342] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/28/2020] [Indexed: 11/18/2022]
Abstract
Cervical carcinoma is the third most common cause of cancer in women with a significant challenge in clinical treatment. Human papillomavirus (HPV) is strongly responsible for cervical carcinoma. Here, we show the increased expression level of heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) in HPV-associated cervical cancer cells including HeLa, Caski, and SiHa cells, especially in HeLa cells. We provide the evidence that the expression of HNRNPA1 is closely related to HeLa cell proliferation, invasion, and migration. Emerging evidence show that histone modifications account for gene expression. Moreover, our results indicate that HNRNPA1 could be regulated by p300 through p300-mediated lysine crotonylation. Inhibition of p300 downregulated both the lysine crotonylation level and the HNRNPA1 expression. And p300-mediated lysine crotonylation participates in the regulation of HNRNPA1 on HeLa cell proliferation, invasion, and migration. Collectively, our study uncovers that p300-mediated lysine crotonylation enhances expression of HNRNPA1 to promote the proliferation, invasion, and migration of HeLa cells.
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39
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Zhang N, Yang Z, Liang W, Liu M. Global Proteomic Analysis of Lysine Crotonylation in the Plant Pathogen Botrytis cinerea. Front Microbiol 2020; 11:564350. [PMID: 33193151 PMCID: PMC7644960 DOI: 10.3389/fmicb.2020.564350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023] Open
Abstract
Lysine crotonylation (Kcr), a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kcr are unknown in B. cinerea or any other plant fungal pathogens. Here, we comprehensively evaluated the crotonylation proteome of B. cinerea and identified 3967 Kcr sites in 1041 proteins, which contained 9 types of modification motifs. Our results show that although the crotonylation was largely conserved, different organisms contained distinct crotonylated proteins with unique functions. Bioinformatics analysis demonstrated that the majority of crotonylated proteins were distributed in cytoplasm (35%), mitochondria (26%), and nucleus (22%). The identified proteins were found to be involved in various metabolic and cellular processes, such as cytoplasmic translation and structural constituent of ribosome. Particularly, 26 crotonylated proteins participated in the pathogenicity of B. cinerea, suggesting a significant role for Kcr in this process. Protein interaction network analysis demonstrated that many protein interactions are regulated by crotonylation. Furthermore, our results show that different nutritional conditions had a significant influence on the Kcr levels of B. cinerea. These data represent the first report of the crotonylome of B. cinerea and provide a good foundation for further explorations of the role of Kcr in plant fungal pathogens.
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Affiliation(s)
- Ning Zhang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Zhenzhou Yang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mengjie Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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40
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Wang Q, Verma J, Vidan N, Wang Y, Tucey TM, Lo TL, Harrison PF, See M, Swaminathan A, Kuchler K, Tscherner M, Song J, Powell DR, Sopta M, Beilharz TH, Traven A. The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen. Cell Rep 2020; 31:107528. [PMID: 32320659 DOI: 10.1016/j.celrep.2020.107528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/31/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of multiple histone acylations diversifies transcriptional control by metabolism, but their functions are incompletely defined. Here we report evidence of histone crotonylation in the human fungal pathogen Candida albicans. We define the enzymes that regulate crotonylation and show its dynamic control by environmental signals: carbon sources, the short-chain fatty acids butyrate and crotonate, and cell wall stress. Crotonate regulates stress-responsive transcription and rescues C. albicans from cell wall stress, indicating broad impact on cell biology. The YEATS domain crotonylation readers Taf14 and Yaf9 are required for C. albicans virulence, and Taf14 controls gene expression, stress resistance, and invasive growth via its chromatin reader function. Blocking the Taf14 C terminus with a tag reduced virulence, suggesting that inhibiting Taf14 interactions with chromatin regulators impairs function. Our findings shed light on the regulation of histone crotonylation and the functions of the YEATS proteins in eukaryotic pathogen biology and fungal infections.
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Affiliation(s)
- Qi Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Jiyoti Verma
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Nikolina Vidan
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia; Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Yanan Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Timothy M Tucey
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Tricia L Lo
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Paul F Harrison
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Michael See
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Karl Kuchler
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Michael Tscherner
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Jiangning Song
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Mary Sopta
- Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia.
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41
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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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Yu H, Bu C, Liu Y, Gong T, Liu X, Liu S, Peng X, Zhang W, Peng Y, Yang J, He L, Zhang Y, Yi X, Yang X, Sun L, Shang Y, Cheng Z, Liang J. Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair. SCIENCE ADVANCES 2020; 6:eaay4697. [PMID: 32201722 PMCID: PMC7069697 DOI: 10.1126/sciadv.aay4697] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/17/2019] [Indexed: 05/15/2023]
Abstract
Previously, we reported that chromodomain Y-like (CDYL) acts as a crotonyl-coenzyme A hydratase and negatively regulates histone crotonylation (Kcr). However, the global CDYL-regulated crotonylome remains unclear. Here, we report a large-scale proteomics analysis for protein Kcr. We identify 14,311 Kcr sites across 3734 proteins in HeLa cells, providing by far the largest crotonylome dataset. We show that depletion of CDYL alters crotonylome landscape affecting diverse cellular pathways. Specifically, CDYL negatively regulated Kcr of RPA1, and mutation of the Kcr sites of RPA1 impaired its interaction with single-stranded DNA and/or with components of resection machinery, supporting a key role of RPA1 Kcr in homologous recombination DNA repair. Together, our study indicates that protein crotonylation has important implication in various pathophysiological processes.
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Affiliation(s)
- Huajing Yu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Yuncheng Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianyu Gong
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaojun Peng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Wenting Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Shang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
- Corresponding author. (J.L.); (Z.C.)
| | - Jing Liang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Corresponding author. (J.L.); (Z.C.)
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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: 76] [Impact Index Per Article: 15.2] [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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44
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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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45
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Sun J, Qiu C, Qian W, Wang Y, Sun L, Li Y, Ding Z. Ammonium triggered the response mechanism of lysine crotonylome in tea plants. BMC Genomics 2019; 20:340. [PMID: 31060518 PMCID: PMC6501322 DOI: 10.1186/s12864-019-5716-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Lysine crotonylation, as a novel evolutionarily conserved type of post-translational modifications, is ubiquitous and essential in cell biology. However, its functions in tea plants are largely unknown, and the full functions of lysine crotonylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Our study attempts to describe the global profiling of nonhistone lysine crotonylation in tea leaves and to explore how ammonium (NH4+) triggers the response mechanism of lysine crotonylome in tea plants. RESULTS Here, we performed the global analysis of crotonylome in tea leaves under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 lysine crotonylation sites on 971 proteins were identified, of which contained in 15 types of crotonylated motifs. Most of crotonylated proteins were located in chloroplast (37%) and cytoplasm (33%). Compared with NH4+ deficiency, 120 and 151 crotonylated proteins were significantly changed at 3 h and 3 days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed crotonylated proteins participated in diverse biological processes such as photosynthesis (PsbO, PsbP, PsbQ, Pbs27, PsaN, PsaF, FNR and ATPase), carbon fixation (rbcs, rbcl, TK, ALDO, PGK and PRK) and amino acid metabolism (SGAT, GGAT2, SHMT4 and GDC), suggesting that lysine crotonylation played important roles in these processes. Moreover, the protein-protein interaction analysis revealed that the interactions of identified crotonylated proteins diversely involved in photosynthesis, carbon fixation and amino acid metabolism. Interestingly, a large number of enzymes were crotonylated, such as Rubisco, TK, SGAT and GGAT, and their activities and crotonylation levels changed significantly by sensing ammonium, indicating a potential function of crotonylation in the regulation of enzyme activities. CONCLUSIONS The results indicated that the crotonylated proteins had a profound influence on metabolic process of tea leaves in response to NH4+ deficiency/resupply, which mainly involved in diverse aspects of primary metabolic processes by sensing NH4+, especially in photosynthesis, carbon fixation and amino acid metabolism. The data might serve as important resources for exploring the roles of lysine crotonylation in N metabolism of tea plants. Data were available via ProteomeXchange with identifier PXD011610.
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Affiliation(s)
- Jianhao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, 250000, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
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46
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Gately S. Human Microbiota and Personalized Cancer Treatments: Role of Commensal Microbes in Treatment Outcomes for Cancer Patients. Cancer Treat Res 2019; 178:253-264. [PMID: 31209849 DOI: 10.1007/978-3-030-16391-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The human gut microbiota consists of about 3.8 × 1013 microorganisms that play an essential role in health, metabolism, and immunomodulation. These gut microbes alter therapeutic response and toxicity to cancer therapies including cytotoxic chemotherapy, radiation therapy, kinase inhibitors, and immunotherapy agents. The gut microbiota generates short-chain fatty acids that are significant regulators of histone post-translational modifications that fundamentally regulate gene expression, linking the microbiota to cellular metabolism and transcriptional regulation. The short-chain fatty acids not only act locally but can be taken up in the blood stream to inhibit the activity of histone deacetylases, regulate gene expression in distant organs as well as the effector function of CD8+ T cells. Cancer and the treatments for it negatively impact the microbiome often resulting in dysbiosis. This can diminish a patient's response to treatment as well as increase systemic toxicities from these therapies. In addition to the gut microbiota, microbes have been detected in tumors that can modulate chemotherapeutic drug response and can result in immune suppression. The gut microbiota and tumor-associated bacteria may be a significant contributor to the interindividual differences and heterogeneous responses to cancer therapies and drug tolerability and strategies that support and/or manipulate the microbiota to improve therapeutic outcome is an emerging area for personalized cancer treatment.
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Affiliation(s)
- Stephen Gately
- Translational Drug Development (TD2), Scottsdale, AZ, USA.
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Yang Q, Li Y, Apaliya MT, Zheng X, Serwah BNA, Zhang X, Zhang H. The Response of Rhodotorula mucilaginosa to Patulin Based on Lysine Crotonylation. Front Microbiol 2018; 9:2025. [PMID: 30233516 PMCID: PMC6129574 DOI: 10.3389/fmicb.2018.02025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 08/09/2018] [Indexed: 12/26/2022] Open
Abstract
Patulin (PAT) is a mycotoxin produced by some Penicillium, Aspergillus, and Byssochlamys species. Rhodotorula mucilaginosa is able to degrade PAT in vivo as well as in vitro, up till date, the process and molecular mechanism(s) involved patulin degradation still remains unknown. Protein lysine crotonylation (Kcr) plays an important role in regulating chromatin dynamics, gene expression, and metabolic pathways in mammals and eukaryotes. Investigation of the Kcr changes accompanying degradation of patulin in R. mucilaginosa were observed to investigate the mechanisms of patulin inhibition. Tandem mass tag (TMT) labeling and Kcro affinity enrichment, followed by high-resolution LC-MS/MS analysis, were used to perform quantitative lysine crotonylome analysis on R. mucilaginosa. Consequently, 1691 lysine crotonylation sites in 629 protein groups were identified, among which we quantified 1457 sites in 562 proteins. Among the quantified proteins, 79 and 46 crotonylated proteins were up-regulated and down-regulated, respectively. The differentially up expressed modified proteins were mainly involved in tricarboxylic acid cycle and gluconeogenic pathway. The differentially down expressed Kcr proteins were mainly classified to ribosome and carbohydrate transport and metabolism. Bioinformatic analyses were performed to annotate the quantifiable lysine crotonylated targets. Moreover, interaction networks and high confidence domain architectures of crotonylated proteins were investigated with the aid of bioinformatic tools, and these results showed that there was an increase in the number of yeasts with crotonylated proteins. The results also provided information on the various roles of crotonylation, which are involved in PAT degradation.
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Affiliation(s)
- Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, China
| | - Yulin Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, China
| | - Maurice T. Apaliya
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xiangfeng Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | | | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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