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Jiang Y, Yan R, Wang X. PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants. Plant Methods 2024; 20:28. [PMID: 38360730 PMCID: PMC10870457 DOI: 10.1186/s13007-024-01157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological experiments is often time-consuming, expensive, and only a fraction of crotonylated peptides can be identified. This reality highlights the need for efficient and rapid prediction of Kcr sites through computational methods. Currently, several machine learning models exist for predicting Kcr sites in humans, yet models tailored for plants are rare. Furthermore, no downloadable Kcr site predictors or datasets have been developed specifically for plants. To address this gap, it is imperative to integrate existing Kcr sites detected in plant experiments and establish a dedicated computational model for plants. RESULTS Most plant Kcr sites are located on non-histones. In this study, we collected non-histone Kcr sites from five plants, including wheat, tabacum, rice, peanut, and papaya. We then conducted a comprehensive analysis of the amino acid distribution surrounding these sites. To develop a predictive model for plant non-histone Kcr sites, we combined a convolutional neural network (CNN), a bidirectional long short-term memory network (BiLSTM), and attention mechanism to build a deep learning model called PlantNh-Kcr. On both five-fold cross-validation and independent tests, PlantNh-Kcr outperformed multiple conventional machine learning models and other deep learning models. Furthermore, we conducted an analysis of species-specific effect on the PlantNh-Kcr model and found that a general model trained using data from multiple species outperforms species-specific models. CONCLUSION PlantNh-Kcr represents a valuable tool for predicting plant non-histone Kcr sites. We expect that this model will aid in addressing key challenges and tasks in the study of plant crotonylation sites.
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Affiliation(s)
- Yanming Jiang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Taiyuan, 030031, China
| | - Renxiang Yan
- The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, 350002, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350002, China
| | - Xiaofeng Wang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Taiyuan, 030031, China.
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2
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Zhou C, Zeng H, Xiao X, Wang L, Jia L, Shi Y, Zhang M, Fang C, Zeng Y, Wu T, Huang J, Liang X. Global crotonylome identifies EP300-regulated ANXA2 crotonylation in cumulus cells as a regulator of oocyte maturation. Int J Biol Macromol 2024; 259:129149. [PMID: 38176486 DOI: 10.1016/j.ijbiomac.2023.129149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
Lysine crotonylation (Kcr), a newly discovered post-translational modification, played a crucial role in physiology and disease progression. However, the roles of crotonylation in oocyte meiotic resumption remain elusive. As abnormal cumulus cell development will cause oocyte maturation arrest and female infertility, we report that cumulus cells surrounding human meiotic arrested oocytes showed significantly lower crotonylation, which was associated with decreased EP300 expression and blocked cumulus cell expansion. In cultured human cumulus cells, exogenous crotonylation or EP300 activator promoted cell proliferation and reduced cell apoptosis, whereas EP300 knockdown induced the opposite effect. Transcriptome profiling analysis in human cumulus cells indicated that functions of crotonylation were associated with activation of epidermal growth factor receptor (EGFR) pathway. Importantly, we characterized the Kcr proteomics landscape in cumulus cells by LC-MS/MS analysis, and identified that annexin A2 (ANXA2) was crotonylated in cumulus cells in an EP300-dependent manner. Crotonylation of ANXA2 enhanced the ANXA2-EGFR binding, and then activated the EGFR pathway to affect cumulus cell proliferation and apoptosis. Using mouse oocytes IVM model and EP300 knockout mice, we further confirmed that crotonylation alteration in cumulus cells affected the oocyte maturation. Together, our results indicated that EP300-mediated crotonylation is important for cumulus cells functions and oocyte maturation.
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Affiliation(s)
- Chuanchuan Zhou
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Haitao Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China
| | - Xingxing Xiao
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Department of Gynecology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong, 528308, China
| | - Li Wang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Tongren People's Hospital, Guizhou, 554300, China
| | - Lei Jia
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China
| | - Yanan Shi
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China
| | - Minfang Zhang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China
| | - Cong Fang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China
| | - Yanyan Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Taibao Wu
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jiana Huang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Xiaoyan Liang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; GuangDong Engineering Technology Research Center of Fertility Preservation, Guangzhou 510080, Guangdong, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.
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Zhang Y, Ji P, Zhang M, Tran NT, Li S. Large-scale lysine crotonylation analysis reveals the role of TRAF6-Ecsit complex in endoplasmic reticulum stress in mud crab (Scylla paramamosain). Dev Comp Immunol 2023; 148:104898. [PMID: 37531975 DOI: 10.1016/j.dci.2023.104898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
Lysine crotonylation (Kcr) is a newly discovered type of post-translational modification. Although Kcr has been reported in several species, its role in crustaceans remains largely unknown. In this study, Kcr in hemocytes of mud crab (Scylla paramamosain) was characterized using pan anti-crotonyllysine antibody enrichment and high-resolution liquid chromatogram-mass spectrometry analysis after SpTRAF6 or SpEcsit silencing. Altogether, 1,800 Kcr sites with six conserved motifs were identified from 512 proteins. Subcellular localization analysis showed that the identified Kcr proteins were mainly localized to the cytoplasm, nucleus, and mitochondria. The cellular components analysis showed that the 'chromosomal region' was enriched in the hemocytes of SpTRAF6-or SpEcsit-silenced mud crabs. The KEGG and PPI analyses showed that the identified Kcr proteins in the hemocytes SpTRAF6-or SpEcsit-silenced mud crabs were related to the 'protein processing in endoplasmic reticulum'; of which the marker of endoplasmic reticulum stress (Bip) was identified to be crotonylated. These datasets present the first comprehensive analysis of the crotonylome in mud crab hemocytes, providing invaluable insights into the regulatory functions of SpTRAF6 and SpEcsit in Kcr. Additionally, our findings shed light on the potential role of these proteins in activating marker proteins during endoplasmic reticulum stress in invertebrates.
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Affiliation(s)
- Yongsheng Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Peina Ji
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Ming Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, 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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Hou JY, Li N, Wang J, Gao LJ, Chang JS, Cao JM. Histone crotonylation of peripheral blood mononuclear cells is a potential biomarker for diagnosis of colorectal cancer. Epigenetics Chromatin 2023; 16:35. [PMID: 37749610 PMCID: PMC10521402 DOI: 10.1186/s13072-023-00509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/17/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Blood-based tests have public appeal in screening cancers due to their minimally invasive nature, ability to integrate with other routine blood tests, and high compliance. This study aimed to investigate whether certain epigenetic modulation of peripheral blood mononuclear cells (PBMCs) could be a biomarker of colorectal cancer (CRC). RESULTS Western blotting of histones in the PBMCs from 40 colorectal cancer patients and 40 healthy controls was performed to identify the crotonylation sites of proteins. The correlation of crotonylation with tumor staging and diagnostic efficacy were analyzed. Crotonylation of H2BK12 (H2BK12cr) was identified significantly upregulated in the PBMCs of CRC patients compared to healthy controls, and were closely related to distant metastasis (P = 0.0478) and late TNM stage (P = 0.0201). Receiver operator characteristic curve (ROC) analysis demonstrated that the area under curve (AUC) of H2BK12cr was 0.8488, the sensitivity was 70%, and the specificity was 92.5%. The H2BK12cr parameter significantly increased the diagnostic effectiveness of CRC compared with the commercial carcinoembryonic antigen assays. CONCLUSIONS The H2BK12cr level in PBMCs of CRC patients has a potential to be a biomarker for distinguishing CRC patients from healthy controls with the advantages of easy operation and high diagnostic efficacy.
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Affiliation(s)
- Jia-Yi Hou
- Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Ning Li
- Department of Gastrointestinal and Pancreatic Surgery and Hernia and Abdominal Surgery, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Jie 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
| | - Li-Juan Gao
- 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-Song Chang
- 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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chen HX, Wang XC, Hou HT, Wang J, Yang Q, Chen YL, Chen HZ, He GW. Lysine crotonylation of SERCA2a correlates to cardiac dysfunction and arrhythmia in Sirt1 cardiac-specific knockout mice. Int J Biol Macromol 2023; 242:125151. [PMID: 37270127 DOI: 10.1016/j.ijbiomac.2023.125151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Protein post-translational modifications (PTMs) are important regulators of protein functions and produce proteome complexity. SIRT1 has NAD+-dependent deacylation of acyl-lysine residues. The present study aimed to explore the correlation between lysine crotonylation (Kcr) on cardiac function and rhythm in Sirt1 cardiac-specific knockout (ScKO) mice and related mechanism. Quantitative proteomics and bioinformatics analysis of Kcr were performed in the heart tissue of ScKO mice established with a tamoxifen-inducible Cre-loxP system. The expression and enzyme activity of crotonylated protein were assessed by western blot, co-immunoprecipitation, and cell biology experiment. Echocardiography and electrophysiology were performed to investigate the influence of decrotonylation on cardiac function and rhythm in ScKO mice. The Kcr of SERCA2a was significantly increased on Lys120 (1.973 folds). The activity of SERCA2a decreased due to lower binding energy of crotonylated SERCA2a and ATP. Changes in expression of PPAR-related proteins suggest abnormal energy metabolism in the heart. ScKO mice had cardiac hypertrophy, impaired cardiac function, and abnormal ultrastructure and electrophysiological activities. We conclude that knockout of SIRT1 alters the ultrastructure of cardiac myocytes, induces cardiac hypertrophy and dysfunction, causes arrhythmia, and changes energy metabolism by regulating Kcr of SERCA2a. These findings provide new insight into the role of PTMs in heart diseases.
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Affiliation(s)
- Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Xiang-Chong Wang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Hai-Tao Hou
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Jun Wang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Yuan-Lu Chen
- Department of Electrophysiology, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Hou-Zao Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China; Department of Surgery, Oregon Health & Science University, Portland, OR 97239-3098, USA.
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Ma Y, Mu X, Gao R, Zhang Y, Geng Y, Chen X, Yin X, Li F, He J. Maternal exposure to dibutyl phthalate regulates MSH6 crotonylation to impair homologous recombination in fetal oocytes. J Hazard Mater 2023; 455:131540. [PMID: 37167869 DOI: 10.1016/j.jhazmat.2023.131540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Homologous recombination (HR) during early oogenesis repairs programmed double-strand breaks (DSBs) to ensure female fertility and offspring health. The exposure of fetal ovaries to endocrine disrupting chemicals (EDCs) can cause reproductive disorders in the adulthood. The EDC dibutyl phthalate (DBP) is widely distributed in flexible plastic products, leading to ubiquitous human exposure. Here, we report that maternal exposure to DBP caused gross aberrations in meiotic prophase I of fetal oocytes, including delayed progression, impaired DNA damage response, uncoupled localization of DMC1 and RAD51, and decreased HR. However, programmed DSBs were efficiently repaired. DBP exposure negatively regulated lysine crotonylation (Kcr) of MSH6. Similar meiotic defects were observed in fetal ovaries with targeted disruption of Msh6, and mutation of K544cr of MSH6 impaired its association with Ku70, thereby promoting non-homologous end joining (NHEJ) and inhibiting HR. Unlike mature F1 females, F2 female mice exhibited premature follicular activation, precocious puberty, and anxiety-like behaviors. Therefore, DBP can influence early meiotic events, and Kcr of MSH6 may regulate preferential induction of HR or NHEJ for DNA repair during meiosis.
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Affiliation(s)
- Yidan Ma
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyi Mu
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Rufei Gao
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Zhang
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yanqing Geng
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xuemei Chen
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xin Yin
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Fangfang Li
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Junlin He
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China.
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Zhang H, Cai J, Li C, Deng L, Zhu H, Huang T, Zhao J, Zhou J, Deng K, Hong Z, Xia J. Wogonin inhibits latent HIV-1 reactivation by downregulating histone crotonylation. Phytomedicine 2023; 116:154855. [PMID: 37172478 DOI: 10.1016/j.phymed.2023.154855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Wogonin, a flavone isolated from Scutellaria baicalensis Georgi, is a commonly used phytochemical with anti-inflammatory and antitumor properties. However, the antiviral activity of wogonin against human immunodeficiency virus type 1 (HIV-1) has not been reported. PURPOSE The current study aimed to explore whether wogonin can suppress latent HIV-1 reactivation and the mechanism of wogonin in inhibiting proviral HIV-1 transcription. METHODS We assessed the effects of wogonin on HIV-1 reactivation using flow cytometry, cytotoxicity assay, quantitative PCR (qPCR), viral quality assurance (VQA), and western blot analysis. RESULTS Wogonin, a flavone isolated from S. baicalensis, significantly inhibited the reactivation of latent HIV-1 in cellular models and in primary CD4+ T cells from antiretroviral therapy (ART)-suppressed individuals ex vivo. Wogonin exhibited low cytotoxicity and long-lasting inhibition of HIV-1 transcription. Triptolide is a latency-promoting agent (LPA) that inhibits HIV-1 transcription and replication; wogonin had a stronger ability to inhibit HIV-1 latent reactivation than triptolide. Mechanistically, wogonin inhibited the reactivation of latent HIV-1 by inhibiting the expression of p300, a histone acetyltransferase, and decreasing the crotonylation of histone H3/H4 in the HIV-1 promoter region. CONCLUSION Our study found that wogonin is a novel LPA that can inhibit HIV-1 transcription by HIV-1 epigenetic silencing, which could bear promising significance for future applications of HIV-1 functional cure.
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Affiliation(s)
- Haitao Zhang
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China; Ward 1 of infection Department, Shenzhen Third People's Hospital, The Second Hospital Affiliated with the School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jinfeng Cai
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Chunna Li
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Lisi Deng
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Hongqiong Zhu
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Ting Huang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiacong Zhao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jiasheng Zhou
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai Deng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhongsi Hong
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Jinyu Xia
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Zhang XY, Liu ZX, Zhang YF, Xu LX, Chen MK, Zhou YF, Yu J, Li XX, Zhang N. SEPT2 crotonylation promotes metastasis and recurrence in hepatocellular carcinoma and is associated with poor survival. Cell Biosci 2023; 13:63. [PMID: 36949517 PMCID: PMC10032003 DOI: 10.1186/s13578-023-00996-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) metastasis and recurrence lead to therapy failure, which are closely associated with the proteome. However, the role of post-translational modification (PTM) in HCC, especially for the recently discovered lysine crotonylation (Kcr), is elusive. RESULTS We investigated the correlation between crotonylation and HCC in 100 tumor tissues and performed stable isotope labeling by amino acids and liquid chromatography tandem mass spectrometry in HCC cells, and we found that crotonylation was positively correlated with HCC metastasis, and higher crotonylation in HCC cells facilitated cell invasiveness. Through bioinformatic analysis, we found that the crotonylated protein SEPT2 was significantly hypercrotonylated in highly invasive cells, while the decrotonylated mutation of SEPT2-K74 impaired SEPT2 GTPase activity and inhibited HCC metastasis in vitro and in vivo. Mechanistically, SIRT2 decrotonylated SEPT2, and P85α was found to be the downstream effector of SEPT2. Moreover, we identified that SEPT2-K74cr was correlated with poor prognosis and recurrence in HCC patients, thus indicating its clinical potential as an independent prognostic factor. CONCLUSIONS We revealed the role of nonhistone protein crotonylation in regulating HCC metastasis and invasion. Crotonylation facilitated cell invasion through the crotonylated SEPT2-K74-P85α-AKT pathway. High SEPT2-K74 crotonylation predicted poor prognosis and a high recurrence rate in HCC patients. Our study revealed a novel role of crotonylation in promoting HCC metastasis.
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Affiliation(s)
- Xin-Yue Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yi-Fan Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Li-Xia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Meng-Ke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Yu-Feng Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao-Xing Li
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
- Department of Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ning Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
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12
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Wang J, Shen F, Liu F, Zhuang S. Histone Modifications in Acute Kidney Injury. Kidney Dis (Basel) 2022; 8:466-477. [PMID: 36590679 PMCID: PMC9798838 DOI: 10.1159/000527799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022]
Abstract
Background Acute kidney injury (AKI) is a serious clinical problem associated with high morbidity and mortality worldwide. The pathophysiology and pathogenesis of AKI is complex and multifactorial. In recent years, epigenetics has emerged as an important regulatory mechanism in AKI. Summary There are several types of histone modification, including methylation, acetylation, phosphorylation, crotonylation, citrullination, and sumoylation. Histone modifications are associated with the transcription of many genes and activation of multiple signaling pathways that contribute to the pathogenesis of AKI. Thus, targeting histone modification may offer novel strategies to protect kidneys from AKI and enhance kidney repair and recovery. In this review, we summarize recent advances on the modification, regulation, and implication of histone modifications in AKI. Key Messages Histone modifications contribute to the pathogenesis of AKI. Understanding of epigenetic regulation in AKI will aid in establishing the utility of pharmacologic targeting of histone modification as a potential novel therapy for AKI.
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Affiliation(s)
- Jun Wang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fengchen Shen
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Liu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island, USA
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13
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Chen X, Fan B, Fan C, Wang Z, Wangkahart E, Huang Y, Huang Y, Jian J, Wang B. First comprehensive proteome analysis of lysine crotonylation in Streptococcus agalactiae, a pathogen causing meningoencephalitis in teleosts. Proteome Sci 2021; 19:14. [PMID: 34758830 PMCID: PMC8580364 DOI: 10.1186/s12953-021-00182-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
Backgroud Streptococcus agalactiae is a common colonizer of the rectovaginal tract and lead to infectious diseases of neonatal and non-pregnant adults, which also causes infectious disease in fish and a zoonotic risk as well. Lysine crotonylation (Kcr) is a kind of histone post-translational modifications discovered in 2011. In yeast and mammals, Kcr function as potential enhancers and promote gene expression. However, lysine crotonylation in S. agalactiae has not been studied yet. Methods In this study, the crotonylation profiling of fish pathogen, S. agalactiae was investigated by combining affinity enrichment with LC MS/MS. The Kcr modification of several selected proteins were further validated by Western blotting. Results In the present study, we conducted the proteome-wide profiling of Kcr in S. agalactiae and identified 241 Kcr sites from 675 screened proteins for the first time. Bioinformatics analysis showed that 164 sequences were matched to a total of six definitively conserved motifs, and many of them were significantly enriched in metabolic processes, cellular process, and single-organism processes. Moreover, four crotonylation modified proteins were predicted as virulence factors or to being part of the quorum sensing system PTMs on bacteria. The data are available via ProteomeXchange with identifier PXD026445. Conclusions These data provide a promising starting point for further functional research of crotonylation in bacterial virulence in S. agalactiae. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00182-y.
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Affiliation(s)
- Xinjin Chen
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China
| | - Bolin Fan
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China
| | - Chenlong Fan
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China
| | - Zhongliang Wang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China.
| | - Eakapol Wangkahart
- Research Unit of Excellence for Tropical Fisheries and Technology, Division of Fisheries, Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Khamriang Sub-District, Kantarawichai, Mahasarakham, Thailand
| | - Yucong Huang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Huang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jichang Jian
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, PR China. .,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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15
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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: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Lin P, Bai HR, He L, Huang QX, Zeng QH, Pan YZ, Jiang BB, Zhang F, Zhang L, Liu QL. Proteome-wide and lysine crotonylation profiling reveals the importance of crotonylation in chrysanthemum (Dendranthema grandiforum) under low-temperature. BMC Genomics 2021; 22:51. [PMID: 33446097 PMCID: PMC7809856 DOI: 10.1186/s12864-020-07365-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/30/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-translational modification (PTM) with multiple cellular functions. However, lysine crotonylation under low-temperature stress has not been studied. RESULTS Proteome-wide and lysine crotonylation of chrysanthemum at low-temperature was analyzed using TMT (Tandem Mass Tag) labeling, sensitive immuno-precipitation, and high-resolution LC-MS/MS. The results showed that 2017 crotonylation sites were identified in 1199 proteins. Treatment at 4 °C for 24 h and - 4 °C for 4 h resulted in 393 upregulated proteins and 500 downregulated proteins (1.2-fold threshold and P < 0.05). Analysis of biological information showed that lysine crotonylation was involved in photosynthesis, ribosomes, and antioxidant systems. The crotonylated proteins and motifs in chrysanthemum were compared with other plants to obtain orthologous proteins and conserved motifs. To further understand how lysine crotonylation at K136 affected APX (ascorbate peroxidase), we performed a site-directed mutation at K136 in APX. Site-directed crotonylation showed that lysine decrotonylation at K136 reduced APX activity, and lysine complete crotonylation at K136 increased APX activity. CONCLUSION In summary, our study comparatively analyzed proteome-wide and crotonylation in chrysanthemum under low-temperature stress and provided insights into the mechanisms of crotonylation in positively regulated APX activity to reduce the oxidative damage caused by low-temperature stress. These data provided an important basis for studying crotonylation to regulate antioxidant enzyme activity in response to low-temperature stress and a new research ideas for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.
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Affiliation(s)
- Ping Lin
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Hui-Ru Bai
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Ling He
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiu-Xiang Huang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qin-Han Zeng
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuan-Zhi Pan
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Bei-Bei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qing-Lin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, People's Republic of China.
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17
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Luo Y, Zhuan Q, Li J, Du X, Huang Z, Hou Y, Fu X. Procyanidin B2 Improves Oocyte Maturation and Subsequent Development in Type 1 Diabetic Mice by Promoting Mitochondrial Function. Reprod Sci 2020; 27:2211-2222. [PMID: 32748223 DOI: 10.1007/s43032-020-00241-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/06/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes (T1D) results in decreased oocyte quality and compromised early embryonic development. Procyanidin B2 (PB2) is a natural compound extracted from grape seeds and has strong antioxidant activity in vivo. This study evaluated the effect of PB2 on oocyte maturation in diabetic mice. Diabetic mice were induced by streptozotocin (STZ) injection. PB2 was supplemented in the in vitro maturation medium, and the ratio of germinal vesicle breakdown (GVBD) and polar body extrusion (PBE), reactive oxygen species (ROS) levels, mitochondrial function, developmental ability, as well as crotonylation at H4K5 were determined in oocytes. PB2 can promote the extrusion of PBE (88.34% vs. 75.02%, P < 0.05); reduce the generation of ROS (1.12 vs. 1.96, P < 0.05); and improve the level of mitochondrial membrane potential (0.87 vs. 0.79 Δφm, P < 0.05), ATP level (1.31 vs. 0.71 pmol, P < 0.05), and mitochondria temperature (618.25 vs. 697.39 pixels, P < 0.05). The addition of PB2 also improved the level of oocyte crotonylation at H4K5 (crH4K5) (47.26 vs. 59.68 pixels, P < 0.05) and increased the blastocyst rate (61.51% vs. 36.07%, P < 0.05) after parthenogenetic activation. Our results are the first to reveal a role for PB2 in promoting the viability of oocytes by regulating the mitochondrial function. Moreover, we uncover that PB2 can improve the level of crH4K5, which provides a new strategy to combat the decline in oocyte quality of diabetic.
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Affiliation(s)
- Yuxi Luo
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qingrui Zhuan
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jun Li
- Department of Reproductive Medicine, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, Hebei, China
| | - Xingzhu Du
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhengyuan Huang
- Chelsea and Westminster Hospital, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW10 9NH, UK
| | - Yunpeng Hou
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Yuanmingyuan West Rd 2, Haidian District, Beijing, 100193, China
| | - Xiangwei Fu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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18
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Fellows R, Varga-Weisz P. Chromatin dynamics and histone modifications in intestinal microbiota-host crosstalk. Mol Metab 2020; 38:100925. [PMID: 31992511 PMCID: PMC7300386 DOI: 10.1016/j.molmet.2019.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The microbiota in the human gut are an important component of normal physiology that has co-evolved from the earliest multicellular organisms. Therefore, it is unsurprising that there is intimate crosstalk between the microbial world in the gut and the host. Genome regulation through microbiota-host interactions not only affects the host's immunity, but also metabolic health and resilience against cancer. Chromatin dynamics of the host epithelium involving histone modifications and other facets of the epigenetic machinery play an important role in this process. SCOPE OF REVIEW This review discusses recent findings relevant to how chromatin dynamics shape the crosstalk between the microbiota and its host, with a special focus on the role of histone modifications. MAJOR CONCLUSIONS Host-microbiome interactions are important evolutionary drivers and are thus expected to be hardwired into and mould the epigenetic machinery in multicellular organisms. Microbial-derived short-chain fatty acids (SCFA) are dominant determinants of microbiome-host interactions, and the inhibition of histone deacetylases (HDACs) by SCFA is a key mechanism in this process. The discovery of alternative histone acylations, such as crotonylation, in addition to the canonical histone acetylation reveals a new layer of complexity in this crosstalk.
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Affiliation(s)
| | - Patrick Varga-Weisz
- Babraham Institute, Babraham, Cambridge, CB22 3AT, UK; School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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19
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Liao P, Bhattarai N, Cao B, Zhou X, Jung JH, Damera K, Fuselier TT, Thareja S, Wimley WC, Wang B, Zeng SX, Lu H. Crotonylation at serine 46 impairs p53 activity. Biochem Biophys Res Commun 2020; 524:730-735. [PMID: 32035620 PMCID: PMC7703795 DOI: 10.1016/j.bbrc.2020.01.152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 02/03/2023]
Abstract
Post-translational modifications (PTMs) play pivotal roles in controlling the stability and activity of the tumor suppressor p53 in response to distinct stressors. Here we report an unexpected finding of a short chain fatty acid modification of p53 in human cells. Crotonic acid (CA) treatment induces p53 crotonylation, but surprisingly reduces its protein, but not mRNA level, leading to inhibition of p53 activity in a dose dependent fashion. Surprisingly this crotonylation targets serine 46, instead of any predicted lysine residues, of p53, as detected in TCEP-probe labeled crotonylation and anti-crotonylated peptide antibody reaction assays. This is further confirmed by substitution of serine 46 with alanine, which abolishes p53 crotonylation in vitro and in cells. CA increases p53-dependent glycolytic activity, and augments cancer cell proliferation in response to metabolic or DNA damage stress. Since serine 46 is only found in human p53, our studies unveil an unconventional PTM unique for human p53, impairing its activity in response to CA. Because CA is likely produced by the gut microbiome, our results also predict that this type of PTM might play a role in early human colorectal neoplasia development by negating p53 activity without mutation of this tumor suppressor gene.
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Affiliation(s)
- Peng Liao
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Surgery, University of Michigan of Medicine, Ann Arbor, MI, USA
| | - Nimisha Bhattarai
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Bo Cao
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Xiang Zhou
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Cancer Institute of Fudan University-Shanghai Cancer Hospital, Shanghai, China
| | - Ji Hoon Jung
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Korean Pathology, College of Korean Medicine, Kyung Hee Seoul, 02447, South Korea
| | - Krishna Damera
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Taylor T Fuselier
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Suresh Thareja
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Shelya X Zeng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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20
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Wang M, Chang Q, Yang H, Liu Y, Wang C, Hu F, Wei H, Li R. Elevated lysine crotonylation and succinylation in the brains of BTBR mice. Int J Dev Neurosci 2019; 76:61-64. [PMID: 31255717 DOI: 10.1016/j.ijdevneu.2019.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/22/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022] Open
Abstract
The BTBR T + Itpr3tf/J (BTBR) mouse has developmental disorders in the central nervous system and many aberrant neuroanatomical structures. However, identification of the pathological mechanisms underlying these abnormal neuroanatomical structures in the brains of BTBR mice is still lacking. Posttranslational modifications (PTMs) are known to be involved in the regulation of diverse cellular processes, and evidence shows that some types of PTMs are associated with the development of the central nervous system. In this study, we detected four novel PTMs in the cerebral cortex of BTBR mice as compared to C57BL/6 J (B6) mice using western blotting. Results revealed that lysine crotonylation and succinylation were elevated in the cerebral cortex of BTBR mice compared to levels in B6 mice. We speculate that elevated profiles of lysine crotonylation and succinylation may be involved in mechanisms related to neuroanatomical abnormalities in cerebral cortex of BTBR mice.
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Affiliation(s)
- Min Wang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Qiaoqiao Chang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Hua Yang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Yongfeng Liu
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Chunfang Wang
- Shanxi Key Laboratory of Animal and Animal Model of Human Diseases, Taiyuan, China
| | - Fengyun Hu
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Hongen Wei
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Rongshan Li
- Nephrology Division, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
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21
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Wan J, Liu H, Ming L. Lysine crotonylation is involved in hepatocellular carcinoma progression. Biomed Pharmacother 2019; 111:976-982. [PMID: 30841477 DOI: 10.1016/j.biopha.2018.12.148] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 11/25/2022] Open
Abstract
Lysine crotonylation is a new posttranslational modification (PTM) type identified on histones, which is enriched on active gene promoters or potential enhancers in mammalian cell genomes. However, the function of lysine crotonylation in the cancer process is not known. Intriguingly, we found that lysine crotonylation expression is down-regulated in liver, stomach, kidney carcinomas, and up-regulated in thyroid, esophagus, colon, pancreas and lung carcinomas. In hepatocellular carcinoma (HCC), lysine crotonylation expression is correlated with Tumour, Node, and Metastasis (TNM) stage. Besides, the crotonylation level is increased by knocking down HDACs or adding HDACs inhibitor, TSA, and thus inhibits hepatoma cell motility and proliferation. Taken together, our findings opened up a new field for the investigation and understanding of the biological role of lysine crotonylation.
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Affiliation(s)
- Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
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22
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Fellows R, Varga-Weisz P. In vitro Enzymatic Assays of Histone De crotonylation on Recombinant Histones. Bio Protoc 2018; 8:e2924. [PMID: 30283810 PMCID: PMC6166789 DOI: 10.21769/bioprotoc.2924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the effect of inhibitors and estimate kinetic constants.
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Affiliation(s)
| | - Patrick Varga-Weisz
- Babraham Institute, Cambridge, UK.,School of Biological Sciences, University of Essex, Colchester, UK
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23
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Moretti C, Vaiman D, Tores F, Cocquet J. Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells. Epigenetics Chromatin 2016; 9:47. [PMID: 27795737 PMCID: PMC5081929 DOI: 10.1186/s13072-016-0099-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis. RESULTS To determine the transcriptional and chromatin state of the sex chromosomes after meiosis, we re-analyzed ten ChIP-Seq datasets performed on mouse round spermatids and four RNA-seq datasets from male germ cells purified at different stages of spermatogenesis. For this, we used the last version of the genome (mm10/GRCm38) and included reads that map to several genomic locations in order to properly interpret the high proportion of sex chromosome-encoded multicopy genes. Our study shows that coverage of active epigenetic marks H3K4me3 and Kcr is similar on the sex chromosomes and on autosomes. The post-meiotic sex chromatin nevertheless differs from autosomal chromatin in its enrichment in H3K9me3 and its depletion in H3K27me3 and H4 acetylation. We also identified a posttranslational modification, H3K27ac, which specifically accumulates on the Y chromosome. In parallel, we found that the X and Y chromosomes are enriched in genes expressed post-meiotically and display a higher proportion of spermatid-specific genes compared to autosomes. Finally, we observed that portions of chromosome 14 and of the sex chromosomes share specific features, such as enrichment in H3K9me3 and the presence of multicopy genes that are specifically expressed in round spermatids, suggesting that parts of chromosome 14 are under the same evolutionary constraints than the sex chromosomes. CONCLUSIONS Based on our expression and epigenomic studies, we conclude that, after meiosis, the mouse sex chromosomes are no longer silenced but are nevertheless regulated differently than autosomes and accumulate different chromatin marks. We propose that post-meiotic selective constraints are at the basis of the enrichment of spermatid-specific genes and of the peculiar chromatin composition of the sex chromosomes and of parts of chromosome 14.
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Affiliation(s)
- Charlotte Moretti
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Daniel Vaiman
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Frederic Tores
- INSERM U1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Julie Cocquet
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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