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Sin YC, Abernathy B, Yuan ZF, Heier JL, Gonzalez JE, Parker LL, Mashek DG, Chen Y. Sorbate induces lysine sorbylation through noncanonical activities of class I HDACs to regulate the expression of inflammation genes. SCIENCE ADVANCES 2025; 11:eadv1071. [PMID: 40446041 PMCID: PMC12124360 DOI: 10.1126/sciadv.adv1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Accepted: 04/25/2025] [Indexed: 06/02/2025]
Abstract
Environmental factors may affect gene expression through epigenetic modifications of histones and transcription factors. Here, we report that cellular uptake of sorbate, a common food preservative, induces lysine sorbylation (Ksor) in mammalian cells and tissue mediated by the noncanonical activities of class I histone deacetylases (HDAC1-3). We demonstrated that HDAC1-3 catalyze sorbylation upon sorbate uptake and desorbylation in the absence of sorbate both in vitro and in cells. Sorbate uptake in mice livers significantly induced histone Ksor, correlating with decreased expressions of inflammation-response genes. Accordingly, sorbate treatment in macrophage RAW264.7 cells upon lipopolysaccharide (LPS) stimulation dose-dependently down-regulated proinflammatory gene expressions and nitric oxide production. Proteomic profiling identified RelA, a component of the NF-κB complex, and its interacting proteins as bona fide Ksor targets and sorbate treatment significantly decreased NF-κB transcriptional activities in response to LPS stimulation in RAW264.7 cells. Together, our study demonstrated a noncanonical mechanism of sorbate uptake in regulating epigenetic histone modifications and inflammatory gene expression.
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Affiliation(s)
- Yi-Cheng Sin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Program, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Breann Abernathy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Zuo-fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jason L. Heier
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Justin E. Gonzalez
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Laurie L. Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Douglas G. Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Minnesota Twin Cities, Minneapolis, MN, USA
- Institute for the Biology of Aging and Metabolism, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA
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2
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Guo L, Du Y, Li H, He T, Yao L, Yang G, Yang X. Metabolites-mediated posttranslational modifications in cardiac metabolic remodeling: Implications for disease pathology and therapeutic potential. Metabolism 2025; 165:156144. [PMID: 39864796 DOI: 10.1016/j.metabol.2025.156144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 01/20/2025] [Accepted: 01/22/2025] [Indexed: 01/28/2025]
Abstract
The nonenergy - producing functions of metabolism are attracting increasing attention, as metabolic changes are involved in discrete pathways modulating enzyme activity and gene expression. Substantial evidence suggests that myocardial metabolic remodeling occurring during diabetic cardiomyopathy, heart failure, and cardiac pathological stress (e.g., myocardial ischemia, pressure overload) contributes to the progression of pathology. Within the rewired metabolic network, metabolic intermediates and end-products can directly alter protein function and/or regulate epigenetic modifications by providing acyl groups for posttranslational modifications, thereby affecting the overall cardiac stress response and providing a direct link between cellular metabolism and cardiac pathology. This review provides a comprehensive overview of the functional diversity and mechanistic roles of several types of metabolite-mediated histone and nonhistone acylation, namely O-GlcNAcylation, lactylation, crotonylation, β-hydroxybutyrylation, and succinylation, as well as fatty acid-mediated modifications, in regulating physiological processes and contributing to the progression of heart disease. Furthermore, it explores the potential of these modifications as therapeutic targets for disease intervention.
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Affiliation(s)
- Lifei Guo
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; Cadet Team 6 of School of Basic Medicine, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Yuting Du
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China; The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Heng Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China
| | - Li Yao
- Department of Pathology, Xi' an No. 3 Hospital, The Affiliated Hospital of Northwest University, Xi' an 710018, China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China.
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Chang-Le Xi Street #127, Xi' an 710032, China.
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Li S, Duan Y, Luo S, Zhou F, Wu Q, Lu Z. Short-chain fatty acids and cancer. Trends Cancer 2025; 11:154-168. [PMID: 39638744 DOI: 10.1016/j.trecan.2024.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/04/2024] [Accepted: 11/04/2024] [Indexed: 12/07/2024]
Abstract
Short-chain fatty acids (SCFAs), derived from the diet and the microbiota, serve as crucial links between the diet, gut microbiota, metabolism, immunity, and cancer. They function as energy sources through β-oxidation and regulate macromolecular synthesis, G protein-coupled receptor (GPCR) and histone deacetylase (HDAC) activities, protein modifications, signaling pathways, and gene expression in cells within the tumor microenvironment, particularly in tumor and immune cells. The critical role of SCFAs in maintaining normal homeostasis and influencing tumor progression highlights the potential of targeting SCFA-mediated cellular processes for cancer prevention and treatment.
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Affiliation(s)
- Shan Li
- Zhejiang Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang Key Laboratory of Frontier Medical Research on Cancer Metabolism, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China; Institute of Fundamental and Transdisciplinary Research, Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Yixin Duan
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Shudi Luo
- Zhejiang Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang Key Laboratory of Frontier Medical Research on Cancer Metabolism, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China; Institute of Fundamental and Transdisciplinary Research, Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Fangxin Zhou
- Zhejiang Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang Key Laboratory of Frontier Medical Research on Cancer Metabolism, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China; Institute of Fundamental and Transdisciplinary Research, Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Qingang Wu
- Zhejiang Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang Key Laboratory of Frontier Medical Research on Cancer Metabolism, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China; Institute of Fundamental and Transdisciplinary Research, Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Zhimin Lu
- Zhejiang Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang Key Laboratory of Frontier Medical Research on Cancer Metabolism, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China; Institute of Fundamental and Transdisciplinary Research, Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China.
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Chen X, Wu L, Zhang Y, Wang S, Wang S. Importance of benzoyltransferase GcnE and lysine benzoylation of alcohol dehydrogenase AdhB in pathogenesis and aflatoxin production in Aspergillus flavus. mBio 2025; 16:e0266524. [PMID: 39601562 PMCID: PMC11708022 DOI: 10.1128/mbio.02665-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024] Open
Abstract
Lysine benzoylation (Kbz) is a newly identified post-translational modification associated with active transcription and metabolism in eukaryotes. However, whether Kbz exists in pathogenic fungi and its function remains unknown. Here, we demonstrated for the first time that Kbz is present in Aspergillus flavus and identified 60 benzoylated sites on 46 benzoylated proteins by global benzoylome analysis. Our data demonstrated that alcohol dehydrogenase B (AdhB) is regulated by benzoylation on lysine 321 (K321), and mutations of Kbz site in AdhB significantly reduced the alcohol dehydrogenase activity in vivo and in vitro. Both adhB deletion mutant and benzoylated site mutants (K321R and K321A) exhibited similar phenotype, including decreased conidiation and seed colonization, increased sclerotia formation and aflatoxin production, and more sensitive to cell wall damage stress. We also found that GcnE has benzoyltransferase activity in vitro and in vivo, and its repression leads to decreased Kbz level and enzymatic activity of AdhB. The catalytic site E139 is important for the benzoyltransferase function of GcnE. Our study uncovers a previously unknown mechanism by which benzoylation regulates AdhB activity to affect the development, secondary metabolism, pathogenicity, and stress response of A. flavus. Meanwhile, it points out the important role of Kbz in the pathogenicity of pathogenic fungi.IMPORTANCEAspergillus flavus is a ubiquitous opportunistic pathogen of plants and animals, which produces carcinogenic and toxic secondary metabolite aflatoxin. A. flavus and aflatoxin contamination have emerged as a global food safety concern. Currently, post-translational modification plays crucial modulatory roles in the fungal development and virulence, but the role of benzoylation in fungal pathogenicity remains undetermined, which limits the development of prevention and control technique. Here, we first identified 46 benzoylated proteins in A. flavus, and found that benzoyltransferase GcnE exerted effects on pathogenicity and aflatoxin production by regulating the benzoylation of AdhB. This finding not only provided valuable information for prevention and control of A. flavus contamination, but also offered basic knowledge for investigation of the regulation mechanism of secondary metabolism in other fungi.
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Affiliation(s)
- Xuan Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihan Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuqi Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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5
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Affiliation(s)
- Yuen Jian Cheong
- Epigenetics and Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Sophie Trefely
- Epigenetics and Signalling Programmes, Babraham Institute, Cambridge, UK.
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6
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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; 277:133883. [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] [MESH Headings] [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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7
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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 PMCID: PMC12016574 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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8
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Shi H, Cui W, Qin Y, Chen L, Yu T, Lv J. A glimpse into novel acylations and their emerging role in regulating cancer metastasis. Cell Mol Life Sci 2024; 81:76. [PMID: 38315203 PMCID: PMC10844364 DOI: 10.1007/s00018-023-05104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Metastatic cancer is a major cause of cancer-related mortality; however, the complex regulation process remains to be further elucidated. A large amount of preliminary investigations focus on the role of epigenetic mechanisms in cancer metastasis. Notably, the posttranslational modifications were found to be critically involved in malignancy, thus attracting considerable attention. Beyond acetylation, novel forms of acylation have been recently identified following advances in mass spectrometry, proteomics technologies, and bioinformatics, such as propionylation, butyrylation, malonylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, lactylation, among others. These novel acylations play pivotal roles in regulating different aspects of energy mechanism and mediating signal transduction by covalently modifying histone or nonhistone proteins. Furthermore, these acylations and their modifying enzymes show promise regarding the diagnosis and treatment of tumors, especially tumor metastasis. Here, we comprehensively review the identification and characterization of 11 novel acylations, and the corresponding modifying enzymes, highlighting their significance for tumor metastasis. We also focus on their potential application as clinical therapeutic targets and diagnostic predictors, discussing the current obstacles and future research prospects.
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Affiliation(s)
- Huifang Shi
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Weigang Cui
- Central Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Yan Qin
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Lei Chen
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Tao Yu
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
| | - Jie Lv
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China.
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9
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Zhang N, Wang S, Tian H, Li S, Liu L, Li J, Chen D, Zhao S, Yan X, Niaz M, Zhao L, Ren Y, Chen F. Functions of lysine 2-hydroxyisobutyrylation and future perspectives on plants. Proteomics 2023; 23:e2300045. [PMID: 37338329 DOI: 10.1002/pmic.202300045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein post-translational modifications (PTMs) observed in both eukaryotes and prokaryotes. Recent studies suggested that this novel PTM has the potential to regulate different proteins in various pathways. Khib is regulated by lysine acyltransferases and deacylases. This novel PTM reveals interesting connections between modifications and protein physiological functions, including gene transcription, glycolysis and cell growth, enzymic activity, sperm motility, and aging. Here, we review the discovery and the current understanding of this PTM. Then, we outline the networks of complexity of interactions among PTMs in plants, and raise possible directions of this novel PTM for future investigations in plants.
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Affiliation(s)
- Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Sisheng Wang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Tian
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Songgang Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lulu Liu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jiaqi Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Daiying Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Simin Zhao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Xiangning Yan
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Mohsin Niaz
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
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10
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Chen X, Duan Y, Ren Z, Niu T, Xu Q, Wang Z, Zheng L, Wang Y, Chen X, Huang J, Pan Y. Post-Translational Modification β-Hydroxybutyrylation Regulates Ustilaginoidea virens Virulence. Mol Cell Proteomics 2023; 22:100616. [PMID: 37442371 PMCID: PMC10423879 DOI: 10.1016/j.mcpro.2023.100616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Lysine β-hydroxybutyrylation (Kbhb) is an evolutionarily conserved and widespread post-translational modification that is associated with active gene transcription and cellular proliferation. However, its role in phytopathogenic fungi remains unknown. Here, we characterized Kbhb in the rice false smut fungus Ustilaginoidea virens. We identified 2204 Kbhb sites in 852 proteins, which are involved in diverse biological processes. The mitogen-activated protein kinase UvSlt2 is a Kbhb protein, and a strain harboring a point mutation at K72, the Kbhb site of this protein, had decreased UvSlt2 activity and reduced fungal virulence. Molecular dynamic simulations revealed that K72bhb increases the hydrophobic solvent-accessible surface area of UvSlt2, thereby affecting its binding to its substrates. The mutation of K298bhb in the septin UvCdc10 resulted in reduced virulence and altered the subcellular localization of this protein. Moreover, we confirmed that the NAD+-dependent histone deacetylases UvSirt2 and UvSirt5 are the major enzymes that remove Kbhb in U. virens. Collectively, our findings identify regulatory elements of the Kbhb pathway and reveal important roles for Kbhb in regulating protein localization and enzymatic activity. These findings provide insight into the regulation of virulence in phytopathogenic fungi via post-translational modifications.
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Affiliation(s)
- Xiaoyang Chen
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei, China
| | - Yuhang Duan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zhiyong Ren
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Taotao Niu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei, China
| | - Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhaoyun Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei, China
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yaohui Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei, China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaolin Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuemin Pan
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei, China.
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11
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Yang YH, Wen R, Yang N, Zhang TN, Liu CF. Roles of protein post-translational modifications in glucose and lipid metabolism: mechanisms and perspectives. Mol Med 2023; 29:93. [PMID: 37415097 DOI: 10.1186/s10020-023-00684-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
The metabolism of glucose and lipids is essential for energy production in the body, and dysregulation of the metabolic pathways of these molecules is implicated in various acute and chronic diseases, such as type 2 diabetes, Alzheimer's disease, atherosclerosis (AS), obesity, tumor, and sepsis. Post-translational modifications (PTMs) of proteins, which involve the addition or removal of covalent functional groups, play a crucial role in regulating protein structure, localization function, and activity. Common PTMs include phosphorylation, acetylation, ubiquitination, methylation, and glycosylation. Emerging evidence indicates that PTMs are significant in modulating glucose and lipid metabolism by modifying key enzymes or proteins. In this review, we summarize the current understanding of the role and regulatory mechanisms of PTMs in glucose and lipid metabolism, with a focus on their involvement in disease progression associated with aberrant metabolism. Furthermore, we discuss the future prospects of PTMs, highlighting their potential for gaining deeper insights into glucose and lipid metabolism and related diseases.
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Affiliation(s)
- Yu-Hang Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Ri Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China
| | - Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China.
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, No.36, SanHao Street, Liaoning Province, Shenyang City, 110004, China.
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12
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Yao Y, Bade R, Li G, Zhang A, Zhao H, Fan L, Zhu R, Yuan J. Global-Scale Profiling of Differential Expressed Lysine-Lactylated Proteins in the Cerebral Endothelium of Cerebral Ischemia-Reperfusion Injury Rats. Cell Mol Neurobiol 2023; 43:1989-2004. [PMID: 36030297 PMCID: PMC11412193 DOI: 10.1007/s10571-022-01277-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
Acute ischemic stroke (AIS) is a serious threat to human health. Following AIS, cerebral ischemia-reperfusion injury (CIRI) must be treated to improve prognosis. By combining 4D label-free quantitative proteomics with lactylation modification-specific proteomics analysis, we assessed lysine lactylation (Kla) in cortical proteins of a CIRI rat model. We identified a total of 1003 lactylation sites on 469 proteins in this study, gathering quantitative information (PXD034232) on 660 of 310 proteins, which were further classified by cell composition, molecular function, and biological processes. In addition, we analyzed the metabolic pathways, domains, and protein-protein interaction networks. Lastly, we evaluated differentially expressed lysine lactylation sites, determining 49 upregulated proteins and 99 downregulated proteins with 54 upregulated sites and 54 downregulated sites in the experimental group in comparison with the healthy control group. Moreover, we identified the Kla of Scl25a4 and Slc25a5 in the Ca2+ signaling pathway, but the Kla of Vdac1 was eliminated, as confirmed in vivo. Overall, these results provide new insights into lactylation involved in the underlying mechanism of CIRI because this post-translational modification affects the mitochondrial apoptosis pathway and mediates neuronal death. Therefore, this study may enable us to develop new molecules with therapeutic properties, which have both theoretical significance and broad clinical application prospects. A new model of cerebral ischemia-reperfusion injury (CIRI) induced by lactylation through the regulation of key proteins of the Ca2+ signaling pathway.
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Affiliation(s)
- Yuan Yao
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Rengui Bade
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, 014060, China
- Medical College of Neuroscience Institute, School of Medical Technology and Anesthesiology, Baotou Medical College, Baotou, 014060, China
| | - Guotao Li
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
| | - Aoqi Zhang
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Haile Zhao
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, 014060, China
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Runxiu Zhu
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
| | - Jun Yuan
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
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13
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Shui K, Wang C, Zhang X, Ma S, Li Q, Ning W, Zhang W, Chen M, Peng D, Hu H, Fang Z, Guo A, Gao G, Ye M, Zhang L, Xue Y. Small-sample learning reveals propionylation in determining global protein homeostasis. Nat Commun 2023; 14:2813. [PMID: 37198164 DOI: 10.1038/s41467-023-38414-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7-16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.
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Affiliation(s)
- Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xuedi Zhang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qinyu Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Guanjun Gao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, Hubei, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, 210031, Jiangsu, China.
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14
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Shi J, Jia X, He Y, Ma X, Qi X, Li W, Gao SJ, Yan Q, Lu C. Immune evasion strategy involving propionylation by the KSHV interferon regulatory factor 1 (vIRF1). PLoS Pathog 2023; 19:e1011324. [PMID: 37023208 PMCID: PMC10112802 DOI: 10.1371/journal.ppat.1011324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/18/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Post-translational modifications (PTMs) are essential for host antiviral immune response and viral immune evasion. Among a set of novel acylations, lysine propionylation (Kpr) has been detected in both histone and non-histone proteins. However, whether protein propionylation occurs in any viral proteins and whether such modifications regulate viral immune evasion remain elusive. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded viral interferon regulatory factor 1 (vIRF1) can be propionylated in lysine residues, which is required for effective inhibition of IFN-β production and antiviral signaling. Mechanistically, vIRF1 promotes its own propionylation by blocking SIRT6's interaction with ubiquitin-specific peptidase 10 (USP10) leading to its degradation via a ubiquitin-proteasome pathway. Furthermore, vIRF1 propionylation is required for its function to block IRF3-CBP/p300 recruitment and repress the STING DNA sensing pathway. A SIRT6-specific activator, UBCS039, rescues propionylated vIRF1-mediated repression of IFN-β signaling. These results reveal a novel mechanism of viral evasion of innate immunity through propionylation of a viral protein. The findings suggest that enzymes involved in viral propionylation could be potential targets for preventing viral infections.
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Affiliation(s)
- Jiale Shi
- Department of Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xuemei Jia
- Department of Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Yujia He
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xinyue Ma
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xiaoyu Qi
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Wan Li
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Shou-Jiang Gao
- Tumor Virology Program, UPMC Hillman Cancer Center, and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Chun Lu
- Department of Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- Department of Microbiology, Nanjing Medical University, Nanjing, People’s Republic of China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People’s Republic of China
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15
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Effects of the Acetyltransferase p300 on Tumour Regulation from the Novel Perspective of Posttranslational Protein Modification. Biomolecules 2023; 13:biom13030417. [PMID: 36979352 PMCID: PMC10046601 DOI: 10.3390/biom13030417] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
p300 acts as a transcription coactivator and an acetyltransferase that plays an important role in tumourigenesis and progression. In previous studies, it has been confirmed that p300 is an important regulator in regulating the evolution of malignant tumours and it also has extensive functions. From the perspective of non-posttranslational modification, it has been proven that p300 can participate in regulating many pathophysiological processes, such as activating oncogene transcription, promoting tumour cell growth, inducing apoptosis, regulating immune function and affecting embryo development. In recent years, p300 has been found to act as an acetyltransferase that catalyses a variety of protein modification types, such as acetylation, propanylation, butyylation, 2-hydroxyisobutyration, and lactylation. Under the catalysis of this acetyltransferase, it plays its crucial tumourigenic driving role in many malignant tumours. Therefore, the function of p300 acetyltransferase has gradually become a research hotspot. From a posttranslational modification perspective, p300 is involved in the activation of multiple transcription factors and additional processes that promote malignant biological behaviours, such as tumour cell proliferation, migration, and invasion, as well as tumour cell apoptosis, drug resistance, and metabolism. Inhibitors of p300 have been developed and are expected to become novel anticancer drugs for several malignancies. We review the characteristics of the p300 protein and its functional role in tumour from the posttranslational modification perspective, as well as the current status of p300-related inhibitor research, with a view to gaining a comprehensive understanding of p300.
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16
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Characterizing crosstalk in epigenetic signaling to understand disease physiology. Biochem J 2023; 480:57-85. [PMID: 36630129 PMCID: PMC10152800 DOI: 10.1042/bcj20220550] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads to changes in epigenetic marks, such as histone post-translational modifications (PTMs), DNA methylation and chromatin accessibility to regulate gene expression. Crosstalk between different epigenetic mechanisms, such as that between histone PTMs and DNA methylation, leads to an intricate network of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However, further development and wider application of these methods is vital in developing treatments for disorders and pathologies that are driven by epigenetic dysregulation.
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17
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Fu Y, Yu J, Li F, Ge S. Oncometabolites drive tumorigenesis by enhancing protein acylation: from chromosomal remodelling to nonhistone modification. J Exp Clin Cancer Res 2022; 41:144. [PMID: 35428309 PMCID: PMC9013066 DOI: 10.1186/s13046-022-02338-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
AbstractMetabolites are intermediate products of cellular metabolism catalysed by various enzymes. Metabolic remodelling, as a biochemical fingerprint of cancer cells, causes abnormal metabolite accumulation. These metabolites mainly generate energy or serve as signal transduction mediators via noncovalent interactions. After the development of highly sensitive mass spectrometry technology, various metabolites were shown to covalently modify proteins via forms of lysine acylation, including lysine acetylation, crotonylation, lactylation, succinylation, propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation and β-hydroxybutyrylation. These modifications can regulate gene expression and intracellular signalling pathways, highlighting the extensive roles of metabolites. Lysine acetylation is not discussed in detail in this review since it has been broadly investigated. We focus on the nine aforementioned novel lysine acylations beyond acetylation, which can be classified into two categories: histone acylations and nonhistone acylations. We summarize the characteristics and common functions of these acylation types and, most importantly, provide a glimpse into their fine-tuned control of tumorigenesis and potential value in tumour diagnosis, monitoring and therapy.
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18
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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19
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Tang H, Zhan Z, Zhang Y, Huang X. Propionylation of lysine, a new mechanism of short-chain fatty acids affecting bacterial virulence. Am J Transl Res 2022; 14:5773-5784. [PMID: 36105019 PMCID: PMC9452321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Propionic acid (PA) is a major component of short-chain fatty acids produced by Bacteroidetes spp. Lysine propionylation is a novel type of protein regulatory posttranslational modification that is widespread in prokaryotes and eukaryotes, as well as in cellular processes, it affects DNA binding affinity, protein stability, and enzyme activity. In this review of published literature, we provide evidence that the level of propionyl modification is influenced by the concentration of PA and the PA metabolic intermediate (propionyl-CoA) and discuss the possibility of PA affecting enteropathogenic bacterial virulence. The understanding of propionyl modification is helpful to better understand the mechanism of PA-producing Bacteroidetes affecting the virulence of pathogenic intestinal bacteria. It may provide novel choices for the prevention and treatment of pathogenic intestinal bacteria.
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Affiliation(s)
- Hao Tang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ziyang Zhan
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ying Zhang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
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20
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Head PE, Myung S, Chen Y, Schneller JL, Wang C, Duncan N, Hoffman P, Chang D, Gebremariam A, Gucek M, Manoli I, Venditti CP. Aberrant methylmalonylation underlies methylmalonic acidemia and is attenuated by an engineered sirtuin. Sci Transl Med 2022; 14:eabn4772. [PMID: 35613279 PMCID: PMC10468269 DOI: 10.1126/scitranslmed.abn4772] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organic acidemias such as methylmalonic acidemia (MMA) are a group of inborn errors of metabolism that typically arise from defects in the catabolism of amino and fatty acids. Accretion of acyl-CoA species is postulated to underlie disease pathophysiology, but the mechanism(s) remain unknown. Here, we surveyed hepatic explants from patients with MMA and unaffected donors, in parallel with samples from various mouse models of methylmalonyl-CoA mutase deficiency. We found a widespread posttranslational modification, methylmalonylation, that inhibited enzymes in the urea cycle and glycine cleavage pathway in MMA. Biochemical studies and mouse genetics established that sirtuin 5 (SIRT5) controlled the metabolism of MMA-related posttranslational modifications. SIRT5 was engineered to resist acylation-driven inhibition via lysine to arginine mutagenesis. The modified SIRT5 was used to create an adeno-associated viral 8 (AAV8) vector and systemically delivered to mutant and control mice. Gene therapy ameliorated hyperammonemia and reduced global methylmalonylation in the MMA mice.
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Affiliation(s)
- PamelaSara E. Head
- National Institute of General Medical Sciences, NIH, 45 Center Drive MSC 6200 Bethesda, MD, 20892-6200 USA
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Sangho Myung
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Yong Chen
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Jessica L. Schneller
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Cindy Wang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Nicholas Duncan
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Pauline Hoffman
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - David Chang
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Abigael Gebremariam
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Marjan Gucek
- National Heart Lung and Blood Institute, NIH, Building 31, 31 Center Drive Bethesda, MD 20892, USA
| | - Irini Manoli
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
| | - Charles P. Venditti
- National Human Genome Research Institute, NIH, Bethesda, MD, 10 Center Drive Building 10, Room 7S257 Bethesda, MD 20892, USA
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21
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Zhang X, Chen J, Dong Q, Zhu J, Peng R, He C, Li Y, Lin R, Jiang P, Zheng M, Zhang H, Liu S, Chen Z. Lysine Acylation Modification Landscape of Brucella abortus Proteome and its Virulent Proteins. Front Cell Dev Biol 2022; 10:839822. [PMID: 35300419 PMCID: PMC8921143 DOI: 10.3389/fcell.2022.839822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The myriad of posttranslational modifications (PTMs) of proteins that occur in all living cells are crucial to all kinds of biological processes. Brucella is an intracellular parasitic bacterium that can cause chronic diseases in both humans and livestock. To reveal the relationship between PTMs and the virulence and survival of Brucella, we described the first comprehensive multiple PTM-omics atlas of B. abortus 2308. Five PTMs involving lysine, namely 2-hydroxyisobutyrylation, succinylation, crotonylation, acetylation, and malonylation were identified. Nearly 2,000 modified proteins were observed, and these proteins took part in many biological processes, with a variety of molecular functions. In addition, we detected many significant virulence factors of Brucella among the modified proteins. 10 of the 15 T4SS effector proteins were detected with one or more PTMs. Moreover, abundant PTMs were detected in other typical virulence factors. Considering the role of PTMs in various biological processes of Brucella virulence and survival, we propose that the virulence of Brucella is associated with the PTMs of proteins. Taken together, this study provides the first global survey of PTMs in Brucella. This is a prospective starting point for further functional analysis of PTMs during the survival of Brucella in hosts, interpretation of the function of Brucella proteins, and elucidation of the pathogenic mechanism of Brucella.
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Affiliation(s)
- Xi Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Jingjing Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Qiao Dong
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Jinying Zhu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Ruihao Peng
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Chuanyu He
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Yuzhuo Li
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Ruiqi Lin
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Pengfei Jiang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Min Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Shiwei Liu
- Department of Nephrology and Endocrinology, Wangjing Hospital, Chinese Academy of Chinese Medical Science, Beijing, China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China.,Department of Nephrology and Endocrinology, Wangjing Hospital, Chinese Academy of Chinese Medical Science, Beijing, China.,Innovative Institute of Zoonoses, Medical College, Inner Mongolia Minzu University, Tongliao, China
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22
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Xu Y, Shi Z, Bao L. An expanding repertoire of protein acylations. Mol Cell Proteomics 2022; 21:100193. [PMID: 34999219 PMCID: PMC8933697 DOI: 10.1016/j.mcpro.2022.100193] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023] Open
Abstract
Protein post-translational modifications play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important post-translational modifications, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry–based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the 12 main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation, and 2-hydroxyisobutyrylation), including their substrates (histones and nonhistone proteins), regulatory enzymes (writers, readers, and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein–membrane interactions, protein stability, and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease, and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research. Provide a general overview of the 12 main protein acylations. Acylation of viral proteins promotes viral integration and infection. Hyperacylation of histone has antitumous and neuroprotective effects. MS is widely used in the identification of acylation but has its challenges.
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Affiliation(s)
- Yuxuan Xu
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Zhenyu Shi
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Li Bao
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China.
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23
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Li W, Li F, Zhang X, Lin HK, Xu C. Insights into the post-translational modification and its emerging role in shaping the tumor microenvironment. Signal Transduct Target Ther 2021; 6:422. [PMID: 34924561 PMCID: PMC8685280 DOI: 10.1038/s41392-021-00825-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
More and more in-depth studies have revealed that the occurrence and development of tumors depend on gene mutation and tumor heterogeneity. The most important manifestation of tumor heterogeneity is the dynamic change of tumor microenvironment (TME) heterogeneity. This depends not only on the tumor cells themselves in the microenvironment where the infiltrating immune cells and matrix together forming an antitumor and/or pro-tumor network. TME has resulted in novel therapeutic interventions as a place beyond tumor beds. The malignant cancer cells, tumor infiltrate immune cells, angiogenic vascular cells, lymphatic endothelial cells, cancer-associated fibroblastic cells, and the released factors including intracellular metabolites, hormonal signals and inflammatory mediators all contribute actively to cancer progression. Protein post-translational modification (PTM) is often regarded as a degradative mechanism in protein destruction or turnover to maintain physiological homeostasis. Advances in quantitative transcriptomics, proteomics, and nuclease-based gene editing are now paving the global ways for exploring PTMs. In this review, we focus on recent developments in the PTM area and speculate on their importance as a critical functional readout for the regulation of TME. A wealth of information has been emerging to prove useful in the search for conventional therapies and the development of global therapeutic strategies.
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Affiliation(s)
- Wen Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
| | - Feifei Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, 530021, Nanning, Guangxi, China
| | - Xia Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Chuan Xu
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China.
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA.
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24
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Gallego-Jara J, Ortega Á, Lozano Terol G, Sola Martínez RA, Cánovas Díaz M, de Diego Puente T. Bacterial Sirtuins Overview: An Open Niche to Explore. Front Microbiol 2021; 12:744416. [PMID: 34803965 PMCID: PMC8603916 DOI: 10.3389/fmicb.2021.744416] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Sirtuins are deacetylase enzymes widely distributed in all domains of life. Although for decades they have been related only to histones deacetylation in eukaryotic organisms, today they are considered global regulators in both prokaryotes and eukaryotes. Despite the important role of sirtuins in humans, the knowledge about bacterial sirtuins is still limited. Several proteomics studies have shown that bacterial sirtuins deacetylate a large number of lysines in vivo, although the effect that this deacetylation causes in most of them remains unknown. To date, only the regulation of a few bacterial sirtuin substrates has been characterized, being their metabolic roles widely distributed: carbon and nitrogen metabolism, DNA transcription, protein translation, or virulence. One of the most current topics on acetylation and deacetylation focuses on studying stoichiometry using quantitative LC-MS/MS. The results suggest that prokaryotic sirtuins deacetylate at low stoichiometry sites, although more studies are needed to know if it is a common characteristic of bacterial sirtuins and its biological significance. Unlike eukaryotic organisms, bacteria usually have one or few sirtuins, which have been reported to have closer phylogenetic similarity with the human Sirt5 than with any other human sirtuin. In this work, in addition to carrying out an in-depth review of the role of bacterial sirtuins in their physiology, a phylogenetic study has been performed that reveals the evolutionary differences between sirtuins of different bacterial species and even between homologous sirtuins.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa A Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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25
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Thomas SP, Denu JM. Short-chain fatty acids activate acetyltransferase p300. eLife 2021; 10:72171. [PMID: 34677127 PMCID: PMC8585482 DOI: 10.7554/elife.72171] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Short-chain fatty acids (SCFAs) acetate, propionate, and butyrate are produced in large quantities by the gut microbiome and contribute to a wide array of physiological processes. While the underlying mechanisms are largely unknown, many effects of SCFAs have been traced to changes in the cell's epigenetic state. Here, we systematically investigate how SCFAs alter the epigenome. Using quantitative proteomics of histone modification states, we identified rapid and sustained increases in histone acetylation after the addition of butyrate or propionate, but not acetate. While decades of prior observations would suggest that hyperacetylation induced by SCFAs are due to inhibition of histone deacetylases (HDACs), we found that propionate and butyrate instead activate the acetyltransferase p300. Propionate and butyrate are rapidly converted to the corresponding acyl-CoAs which are then used by p300 to catalyze auto-acylation of the autoinhibitory loop, activating the enzyme for histone/protein acetylation. This data challenges the long-held belief that SCFAs mainly regulate chromatin by inhibiting HDACs, and instead reveals a previously unknown mechanism of HAT activation that can explain how an influx of low levels of SCFAs alters global chromatin states.
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Affiliation(s)
- Sydney P Thomas
- Wisconsin Institute for Discovery, Madison, United States.,Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, United States
| | - John M Denu
- Wisconsin Institute for Discovery, Madison, United States.,Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, United States.,Morgridge Institute for Research, Madison, United States
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26
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Chen X, Xu Q, Duan Y, Liu H, Chen X, Huang J, Luo C, Zhou DX, Zheng L. Ustilaginoidea virens modulates lysine 2-hydroxyisobutyrylation in rice flowers during infection. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1801-1814. [PMID: 34245484 DOI: 10.1111/jipb.13149] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The post-translational modification lysine 2-hydroxyisobutyrylation (Khib ) plays an important role in gene transcription, metabolism, and enzymatic activity. Khib sites have been identified in rice (Oryza sativa). However, the Khib status of proteins in rice flowers during pathogen infection remains unclear. Here, we report a comprehensive identification of Khib -modified proteins in rice flowers, and the changes in these proteins during infection with the fungal pathogen Ustilaginoidea virens. By using a tandem mass tag-based quantitative proteomics approach, we identified 2,891 Khib sites on 964 proteins in rice flowers. Our data demonstrated that 2-hydroxyisobutyrylated proteins are involved in diverse biological processes. Khib levels were substantially reduced upon infection with U. virens. Chromatin immunoprecipitation polymerase chain reaction (PCR) and reverse transcription quantitative PCR analyses revealed that histone Khib is involved in the expression of disease-resistance genes. More importantly, most quantified sites on core histones H3 were downregulated upon U. virens infection. In addition, the histone deacetylases HDA705, HDA716, SRT1, and SRT2 are involved in the removal of Khib marks in rice. HDA705 was further confirmed to negatively regulate rice disease resistance to pathogens U. virens, Magnaporthe oryzae, and Xanthomonas oryzae pv. oryzae (Xoo). Our data suggest that U. virens could modulate Khib in rice flowers during infection.
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Affiliation(s)
- Xiaoyang Chen
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhang Duan
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolin Chen
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junbin Huang
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaoxi Luo
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Lu Zheng
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
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27
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021. [PMID: 34159701 DOI: 10.5252/embr.202152774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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28
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021; 22:e52774. [PMID: 34159701 PMCID: PMC8406397 DOI: 10.15252/embr.202152774] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)University of CantabriaSantanderSpain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Faculty of BiologyLudwig‐Maximilians Universität MünchenPlanegg‐MartinsriedGermany
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29
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Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies. Sci Rep 2021; 11:12795. [PMID: 34140538 PMCID: PMC8211816 DOI: 10.1038/s41598-021-91359-0] [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: 04/06/2020] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
The collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromatin immunoprecipitation (ChIP)-based approach called Epigenetics-IDentifier (Epi-ID), we aimed to identify regulators of crotonylation, succinylation and butyrylation in thousands of yeast mutants simultaneously. However, highly correlative results led us to further investigate the specificity of the pan-K-acyl antibodies used in our Epi-ID studies. This revealed cross-reactivity and lack of specificity of pan-K-acyl antibodies in various assays. Our findings suggest that the antibodies might recognize histone acetylation in vivo, in addition to histone acylation, due to the vast overabundance of acetylation compared to other acylation modifications in cells. Consequently, our Epi-ID screen mostly identified factors affecting histone acetylation, including known (e.g. GCN5, HDA1, and HDA2) and unanticipated (MET7, MTF1, CLB3, and RAD26) factors, expanding the repertoire of acetylation regulators. Antibody-independent follow-up experiments on the Gcn5-Ada2-Ada3 (ADA) complex revealed that, in addition to acetylation and crotonylation, ADA has the ability to butyrylate histones. Thus, our Epi-ID screens revealed limits of using pan-K-acyl antibodies in epigenetics research, expanded the repertoire of regulators of histone acetylation, and attributed butyrylation activity to the ADA complex.
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30
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Li A, Deng Y, Tan Y, Chen M. A Transfer Learning-Based Approach for Lysine Propionylation Prediction. Front Physiol 2021; 12:658633. [PMID: 33967828 PMCID: PMC8096918 DOI: 10.3389/fphys.2021.658633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Lysine propionylation is a newly discovered posttranslational modification (PTM) and plays a key role in the cellular process. Although proteomics techniques was capable of detecting propionylation, large-scale detection was still challenging. To bridge this gap, we presented a transfer learning-based method for computationally predicting propionylation sites. The recurrent neural network-based deep learning model was trained firstly by the malonylation and then fine-tuned by the propionylation. The trained model served as feature extractor where protein sequences as input were translated into numerical vectors. The support vector machine was used as the final classifier. The proposed method reached a matthews correlation coefficient (MCC) of 0.6615 on the 10-fold crossvalidation and 0.3174 on the independent test, outperforming state-of-the-art methods. The enrichment analysis indicated that the propionylation was associated with these GO terms (GO:0016620, GO:0051287, GO:0003735, GO:0006096, and GO:0005737) and with metabolism. We developed a user-friendly online tool for predicting propoinylation sites which is available at http://47.113.117.61/.
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Affiliation(s)
- Ang Li
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yingwei Deng
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yan Tan
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
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31
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Ding Q, Zhang Z, Li Y, Liu H, Hao Q, Yang Y, Ringø E, Olsen RE, Clarke JL, Ran C, Zhou Z. Propionate induces intestinal oxidative stress via Sod2 propionylation in zebrafish. iScience 2021; 24:102515. [PMID: 34142031 PMCID: PMC8188496 DOI: 10.1016/j.isci.2021.102515] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/17/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022] Open
Abstract
Propionate and propionyl-CoA accumulation have been associated with the development of mitochondrial dysfunction. In this study, we show that propionate induces intestinal damage in zebrafish when fed a high-fat diet (HFD). The intestinal damage was associated with oxidative stress owing to compromised superoxide dismutase 2 (Sod2) activity. Global lysine propionylation analysis of the intestinal samples showed that Sod2 was propionylated at lysine 132 (K132), and further biochemical assays demonstrated that K132 propionylation suppressed Sod2 activity. In addition, sirtuin 3 (Sirt3) played an important role in regulating Sod2 activity via modulating de-propionylation. Finally, we revealed that intestinal oxidative stress resulting from Sod2 propionylation contributed to compositional change of gut microbiota. Collectively, our results in this study show that there is a link between Sod2 propionylation and oxidative stress in zebrafish intestines and highlight the potential mechanism of intestinal problems associated with high propionate levels. Propionate supplementation in high-fat diet induces intestinal damage Propionate induces oxidative stress via Sod2 propionylation at 132 lysine site Increased Sod2 propionylation is associated with reduced expression of Sirt3 Intestinal oxidative stress alters gut microbiota composition
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Affiliation(s)
- Qianwen Ding
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Li
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongliang Liu
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang Hao
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Einar Ringø
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Rolf Erik Olsen
- Norway-China Joint Lab on Fish Gastrointestinal Microbiota, Institute of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | | | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhou
- China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Lagerwaard B, van der Hoek MD, Hoeks J, Grevendonk L, Nieuwenhuizen AG, Keijer J, de Boer VCJ. Propionate hampers differentiation and modifies histone propionylation and acetylation in skeletal muscle cells. Mech Ageing Dev 2021; 196:111495. [PMID: 33932454 DOI: 10.1016/j.mad.2021.111495] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/19/2022]
Abstract
Protein acylation via metabolic acyl-CoA intermediates provides a link between cellular metabolism and protein functionality. A process in which acetyl-CoA and acetylation are fine-tuned is during myogenic differentiation. However, the roles of other protein acylations remain unknown. Protein propionylation could be functionally relevant because propionyl-CoA can be derived from the catabolism of amino acids and fatty acids and was shown to decrease during muscle differentiation. We aimed to explore the potential role of protein propionylation in muscle differentiation, by mimicking a pathophysiological situation with high extracellular propionate which increases propionyl-CoA and protein propionylation, rendering it a model to study increased protein propionylation. Exposure to extracellular propionate, but not acetate, impaired myogenic differentiation in C2C12 cells and propionate exposure impaired myogenic differentiation in primary human muscle cells. Impaired differentiation was accompanied by an increase in histone propionylation as well as histone acetylation. Furthermore, chromatin immunoprecipitation showed increased histone propionylation at specific regulatory myogenic differentiation sites of the Myod gene. Intramuscular propionylcarnitine levels are higher in old compared to young males and females, possibly indicating increased propionyl-CoA levels with age. The findings suggest a role for propionylation and propionyl-CoA in regulation of muscle cell differentiation and ageing, possibly via alterations in histone acylation.
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Affiliation(s)
- Bart Lagerwaard
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands; TI Food and Nutrition, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
| | - Marjanne D van der Hoek
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands; Applied Research Centre Food and Dairy, Van Hall Larenstein University of Applied Sciences, Leeuwarden, the Netherlands; MCL Academy, Medical Centre Leeuwarden, Leeuwarden, the Netherlands
| | - Joris Hoeks
- Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, 6200 MD, Maastricht, the Netherlands
| | - Lotte Grevendonk
- TI Food and Nutrition, P.O. Box 557, 6700 AN, Wageningen, the Netherlands; Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, 6200 MD, Maastricht, the Netherlands
| | - Arie G Nieuwenhuizen
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Vincent C J de Boer
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands.
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Wang M, Lin H. Understanding the Function of Mammalian Sirtuins and Protein Lysine Acylation. Annu Rev Biochem 2021; 90:245-285. [PMID: 33848425 DOI: 10.1146/annurev-biochem-082520-125411] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein lysine acetylation is an important posttranslational modification that regulates numerous biological processes. Targeting lysine acetylation regulatory factors, such as acetyltransferases, deacetylases, and acetyl-lysine recognition domains, has been shown to have potential for treating human diseases, including cancer and neurological diseases. Over the past decade, many other acyl-lysine modifications, such as succinylation, crotonylation, and long-chain fatty acylation, have also been investigated and shown to have interesting biological functions. Here, we provide an overview of the functions of different acyl-lysine modifications in mammals. We focus on lysine acetylation as it is well characterized, and principles learned from acetylation are useful for understanding the functions of other lysine acylations. We pay special attention to the sirtuins, given that the study of sirtuins has provided a great deal of information about the functions of lysine acylation. We emphasize the regulation of sirtuins to illustrate that their regulation enables cells to respond to various signals and stresses.
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Affiliation(s)
- Miao Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA; .,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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Qian H, Wang L, Ma X, Yi X, Wang B, Liang W. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylated Proteins in Fusarium oxysporum. Front Microbiol 2021; 12:623735. [PMID: 33643252 PMCID: PMC7902869 DOI: 10.3389/fmicb.2021.623735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Protein lysine 2-hydroxyisobutyrylation (K hib ), a new type of post-translational modification, occurs in histones and non-histone proteins and plays an important role in almost all aspects of both eukaryotic and prokaryotic living cells. Fusarium oxysporum, a soil-borne fungal pathogen, can cause disease in more than 150 plants. However, little is currently known about the functions of K hib in this plant pathogenic fungus. Here, we report a systematic analysis of 2-hydroxyisobutyrylated proteins in F. oxysporum. In this study, 3782 K hib sites in 1299 proteins were identified in F. oxysporum. The bioinformatics analysis showed that 2-hydroxyisobutyrylated proteins are involved in different biological processes and functions and are located in diverse subcellular localizations. The enrichment analysis revealed that K hib participates in a variety of pathways, including the ribosome, oxidative phosphorylation, and proteasome pathways. The protein interaction network analysis showed that 2-hydroxyisobutyrylated protein complexes are involved in diverse interactions. Notably, several 2-hydroxyisobutyrylated proteins, including three kinds of protein kinases, were involved in the virulence or conidiation of F. oxysporum, suggesting that K hib plays regulatory roles in pathogenesis. Moreover, our study shows that there are different K hib levels of F. oxysporum in conidial and mycelial stages. These findings provide evidence of K hib in F. oxysporum, an important filamentous plant pathogenic fungus, and serve as a resource for further exploration of the potential functions of K hib in Fusarium species and other filamentous pathogenic fungi.
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Affiliation(s)
- Hengwei Qian
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Shandong Normal University, Jinan, China
| | - Lulu Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | | | - Xingling Yi
- Micron Biotechnology Co., Ltd., Hangzhou, China
| | - Baoshan Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Lagerwaard B, Pougovkina O, Bekebrede AF, te Brinke H, Wanders RJ, Nieuwenhuizen AG, Keijer J, de Boer VCJ. Increased protein propionylation contributes to mitochondrial dysfunction in liver cells and fibroblasts, but not in myotubes. J Inherit Metab Dis 2021; 44:438-449. [PMID: 32740932 PMCID: PMC8049071 DOI: 10.1002/jimd.12296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/22/2022]
Abstract
Post-translational protein modifications derived from metabolic intermediates, such as acyl-CoAs, have been shown to regulate mitochondrial function. Patients with a genetic defect in the propionyl-CoA carboxylase (PCC) gene clinically present symptoms related to mitochondrial disorders and are characterised by decreased mitochondrial respiration. Since propionyl-CoA accumulates in PCC deficient patients and protein propionylation can be driven by the level of propionyl-CoA, we hypothesised that protein propionylation could play a role in the pathology of the disease. Indeed, we identified increased protein propionylation due to pathologic propionyl-CoA accumulation in patient-derived fibroblasts and this was accompanied by defective mitochondrial respiration, as was shown by a decrease in complex I-driven respiration. To mimic pathological protein propionylation levels, we exposed cultured fibroblasts, Fao liver cells and C2C12 muscle myotubes to propionate levels that are typically found in these patients. This induced a global increase in protein propionylation and histone protein propionylation and was also accompanied by a decrease in mitochondrial respiration in liver and fibroblasts. However, in C2C12 myotubes propionate exposure did not decrease mitochondrial respiration, possibly due to differences in propionyl-CoA metabolism as compared to the liver. Therefore, protein propionylation could contribute to the pathology in these patients, especially in the liver, and could therefore be an interesting target to pursue in the treatment of this metabolic disease.
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Affiliation(s)
- Bart Lagerwaard
- Human and Animal Physiology, Wageningen University and ResearchWageningenNetherlands
- TI Food and NutritionWageningenNetherlands
| | - Olga Pougovkina
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAcademic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Anna F. Bekebrede
- Human and Animal Physiology, Wageningen University and ResearchWageningenNetherlands
| | - Heleen te Brinke
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAcademic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Ronald J.A. Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAcademic Medical Center, University of AmsterdamAmsterdamNetherlands
- Department of PediatricsEmma Children's Hospital, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Arie G. Nieuwenhuizen
- Human and Animal Physiology, Wageningen University and ResearchWageningenNetherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and ResearchWageningenNetherlands
| | - Vincent C. J. de Boer
- Human and Animal Physiology, Wageningen University and ResearchWageningenNetherlands
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAcademic Medical Center, University of AmsterdamAmsterdamNetherlands
- Department of PediatricsEmma Children's Hospital, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
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Chen X, Li X, Li P, Chen X, Liu H, Huang J, Luo C, Hsiang T, Zheng L. Comprehensive identification of lysine 2-hydroxyisobutyrylated proteins in Ustilaginoidea virens reveals the involvement of lysine 2-hydroxyisobutyrylation in fungal virulence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:409-425. [PMID: 33427395 DOI: 10.1111/jipb.13066] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib ) is a newly identified post-translational modification (PTM) that plays important roles in transcription and cell proliferation in eukaryotes. However, its function remains unknown in phytopathogenic fungi. Here, we performed a comprehensive assessment of Khib in the rice false smut fungus Ustilaginoidea virens, using Tandem Mass Tag (TMT)-based quantitative proteomics approach. A total of 3 426 Khib sites were identified in 977 proteins, suggesting that Khib is a common and complex PTM in U. virens. Our data demonstrated that the 2-hydroxyisobutyrylated proteins are involved in diverse biological processes. Network analysis of the modified proteins revealed a highly interconnected protein network that included many well-studied virulence factors. We confirmed that the Zn-binding reduced potassium dependency3-type histone deacetylase (UvRpd3) is a major enzyme that removes 2-hydroxyisobutyrylation and acetylation in U. virens. Notably, mutations of Khib sites in the mitogen-activated protein kinase (MAPK) UvSlt2 significantly reduced fungal virulence and decreased the enzymatic activity of UvSlt2. Molecular dynamics simulations demonstrated that 2-hydroxyisobutyrylation in UvSlt2 increased the hydrophobic solvent-accessible surface area and thereby affected binding between the UvSlt2 enzyme and its substrates. Our findings thus establish Khib as a major post-translational modification in U. virens and point to an important role for Khib in the virulence of this phytopathogenic fungus.
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Affiliation(s)
- Xiaoyang Chen
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiabing Li
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pingping Li
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolin Chen
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junbin Huang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaoxi Luo
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lu Zheng
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
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RAM-PGK: Prediction of Lysine Phosphoglycerylation Based on Residue Adjacency Matrix. Genes (Basel) 2020; 11:genes11121524. [PMID: 33419274 PMCID: PMC7766696 DOI: 10.3390/genes11121524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 11/29/2022] Open
Abstract
Background: Post-translational modification (PTM) is a biological process that is associated with the modification of proteome, which results in the alteration of normal cell biology and pathogenesis. There have been numerous PTM reports in recent years, out of which, lysine phosphoglycerylation has emerged as one of the recent developments. The traditional methods of identifying phosphoglycerylated residues, which are experimental procedures such as mass spectrometry, have shown to be time-consuming and cost-inefficient, despite the abundance of proteins being sequenced in this post-genomic era. Due to these drawbacks, computational techniques are being sought to establish an effective identification system of phosphoglycerylated lysine residues. The development of a predictor for phosphoglycerylation prediction is not a first, but it is necessary as the latest predictor falls short in adequately detecting phosphoglycerylated and non-phosphoglycerylated lysine residues. Results: In this work, we introduce a new predictor named RAM-PGK, which uses sequence-based information relating to amino acid residues to predict phosphoglycerylated and non-phosphoglycerylated sites. A benchmark dataset was employed for this purpose, which contained experimentally identified phosphoglycerylated and non-phosphoglycerylated lysine residues. From the dataset, we extracted the residue adjacency matrix pertaining to each lysine residue in the protein sequences and converted them into feature vectors, which is used to build the phosphoglycerylation predictor. Conclusion: RAM-PGK, which is based on sequential features and support vector machine classifiers, has shown a noteworthy improvement in terms of performance in comparison to some of the recent prediction methods. The performance metrics of the RAM-PGK predictor are: 0.5741 sensitivity, 0.6436 specificity, 0.0531 precision, 0.6414 accuracy, and 0.0824 Mathews correlation coefficient.
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38
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Høgh RI, Møller SH, Jepsen SD, Mellergaard M, Lund A, Pejtersen M, Fitzner E, Andresen L, Skov S. Metabolism of short-chain fatty acid propionate induces surface expression of NKG2D ligands on cancer cells. FASEB J 2020; 34:15531-15546. [PMID: 32996653 DOI: 10.1096/fj.202000162r] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 08/30/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
SCFAs are primarily produced in the colon by bacterial fermentation of nondigestible carbohydrates. Besides providing energy, SCFAs can suppress development of colon cancer. The mechanism, however, remains elusive. Here, we demonstrate that the SCFA propionate upregulates surface expression of the immune stimulatory NKG2D ligands, MICA/B by imposing metabolic changes in dividing cells. Propionate-mediated MICA/B expression did not rely on GPR41/GPR43 receptors but depended on functional mitochondria. By siRNA-directed knockdown, we could further link phosphoenolpyruvate carboxykinase (PEPCK), the rate-limiting enzyme in gluconeogenesis to propionate regulation of MICA/B expression. Moreover, knockdown of Rictor and specific mTOR inhibitors implicated mTORC2 activity with metabolic changes that control MICA/B expression. SCFAs are precursors to short-chain acyl-CoAs that are used for histone acylation thereby linking the metabolic state to chromatin structure and gene expression. Propionate increased the overall acetylation and propionylation and inhibition of lysine acetyltransferases (KATs) that are responsible for adding acyl-CoAs to histones reduced propionate-mediated MICA/B expression, suggesting that propionate-induced acylation increases MICA/B expression. Notably, propionate upregulated MICA/B surface expression on colon cancer cells in an acylation-dependent manner; however, the impact of mitochondrial metabolism on MICA/B expression was different in colon cancer cells compared with Jurkat cells, suggesting that continuous exposure to propionate in the colon may provide an enhanced capacity to metabolize propionate. Together, our findings support that propionate causes metabolic changes resulting in NKG2D ligand surface expression, which holds potential as an immune activating anticancer therapy.
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Affiliation(s)
- Rikke Illum Høgh
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofie Hedlund Møller
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Dam Jepsen
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maiken Mellergaard
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Astrid Lund
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikala Pejtersen
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emil Fitzner
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Andresen
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Skov
- Laboratory of Immunology, Section for Experimental Animal Models, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Haws SA, Leech CM, Denu JM. Metabolism and the Epigenome: A Dynamic Relationship. Trends Biochem Sci 2020; 45:731-747. [DOI: 10.1016/j.tibs.2020.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
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Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly identified post-translational modifications (PTMs) primitively identified by mass spectrometry (MS). Research in animals suggests that histone Khib is related to regulation of chromatin and cellular functions. However, there is no review to summarize and elaborate on the current understanding of Khib. In this review, we start with the basic description of Khib, such as sequence preference and subcellular localization. We then analyze the lysine 2-hydroxyisobutyrylated sites with the purpose of learning its functions and activities. We finally discuss the regulation toward Khib and the way it regulates, thus opening an avenue for us to illustrate the diverse cellular metabolites associated with (Khib).
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Affiliation(s)
- Shaoying Huang
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
| | - Donge Tang
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
| | - Yong Dai
- Department of Clinical Medical Research Center, Shenzhen People's Hospital, Shenzhen, CHN
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Trefely S, Lovell CD, Snyder NW, Wellen KE. Compartmentalised acyl-CoA metabolism and roles in chromatin regulation. Mol Metab 2020; 38:100941. [PMID: 32199817 PMCID: PMC7300382 DOI: 10.1016/j.molmet.2020.01.005] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many metabolites serve as important signalling molecules to adjust cellular activities and functions based on nutrient availability. Links between acetyl-CoA metabolism, histone lysine acetylation, and gene expression have been documented and studied over the past decade. In recent years, several additional acyl modifications to histone lysine residues have been identified, which depend on acyl-coenzyme A thioesters (acyl-CoAs) as acyl donors. Acyl-CoAs are intermediates of multiple distinct metabolic pathways, and substantial evidence has emerged that histone acylation is metabolically sensitive. Nevertheless, the metabolic sources of acyl-CoAs used for chromatin modification in most cases remain poorly understood. Elucidating how these diverse chemical modifications are coupled to and regulated by cellular metabolism is important in deciphering their functional significance. SCOPE OF REVIEW In this article, we review the metabolic pathways that produce acyl-CoAs, as well as emerging evidence for functional roles of diverse acyl-CoAs in chromatin regulation. Because acetyl-CoA has been extensively reviewed elsewhere, we will focus on four other acyl-CoA metabolites integral to major metabolic pathways that are also known to modify histones: succinyl-CoA, propionyl-CoA, crotonoyl-CoA, and butyryl-CoA. We also briefly mention several other acyl-CoA species, which present opportunities for further research; malonyl-CoA, glutaryl-CoA, 3-hydroxybutyryl-CoA, 2-hydroxyisobutyryl-CoA, and lactyl-CoA. Each acyl-CoA species has distinct roles in metabolism, indicating the potential to report shifts in the metabolic status of the cell. For each metabolite, we consider the metabolic pathways in which it participates and the nutrient sources from which it is derived, the compartmentalisation of its metabolism, and the factors reported to influence its abundance and potential nuclear availability. We also highlight reported biological functions of these metabolically-linked acylation marks. Finally, we aim to illuminate key questions in acyl-CoA metabolism as they relate to the control of chromatin modification. MAJOR CONCLUSIONS A majority of acyl-CoA species are annotated to mitochondrial metabolic processes. Since acyl-CoAs are not known to be directly transported across mitochondrial membranes, they must be synthesized outside of mitochondria and potentially within the nucleus to participate in chromatin regulation. Thus, subcellular metabolic compartmentalisation likely plays a key role in the regulation of histone acylation. Metabolite tracing in combination with targeting of relevant enzymes and transporters will help to map the metabolic pathways that connect acyl-CoA metabolism to chromatin modification. The specific function of each acyl-CoA may be determined in part by biochemical properties that affect its propensity for enzymatic versus non-enzymatic protein modification, as well as the various enzymes that can add, remove and bind each modification. Further, competitive and inhibitory effects of different acyl-CoA species on these enzymes make determining the relative abundance of acyl-CoA species in specific contexts important to understand the regulation of chromatin acylation. An improved and more nuanced understanding of metabolic regulation of chromatin and its roles in physiological and disease-related processes will emerge as these questions are answered.
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Affiliation(s)
- Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Short-chain fatty acid, acylation and cardiovascular diseases. Clin Sci (Lond) 2020; 134:657-676. [PMID: 32219347 DOI: 10.1042/cs20200128] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Metabolic dysfunction is a fundamental core mechanism underlying CVDs. Previous studies generally focused on the roles of long-chain fatty acids (LCFAs) in CVDs. However, a growing body of study has implied that short-chain fatty acids (SCFAs: namely propionate, malonate, butyrate, 2-hydroxyisobutyrate (2-HIBA), β-hydroxybutyrate, crotonate, succinate, and glutarate) and their cognate acylations (propionylation, malonylation, butyrylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, crotonylation, succinylation, and glutarylation) participate in CVDs. Here, we attempt to provide an overview landscape of the metabolic pattern of SCFAs in CVDs. Especially, we would focus on the SCFAs and newly identified acylations and their roles in CVDs, including atherosclerosis, hypertension, and heart failure.
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Chandra A, Sharma A, Dehzangi A, Shigemizu D, Tsunoda T. Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. BMC Mol Cell Biol 2019; 20:57. [PMID: 31856704 PMCID: PMC6923822 DOI: 10.1186/s12860-019-0240-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The biological process known as post-translational modification (PTM) is a condition whereby proteomes are modified that affects normal cell biology, and hence the pathogenesis. A number of PTMs have been discovered in the recent years and lysine phosphoglycerylation is one of the fairly recent developments. Even with a large number of proteins being sequenced in the post-genomic era, the identification of phosphoglycerylation remains a big challenge due to factors such as cost, time consumption and inefficiency involved in the experimental efforts. To overcome this issue, computational techniques have emerged to accurately identify phosphoglycerylated lysine residues. However, the computational techniques proposed so far hold limitations to correctly predict this covalent modification. RESULTS We propose a new predictor in this paper called Bigram-PGK which uses evolutionary information of amino acids to try and predict phosphoglycerylated sites. The benchmark dataset which contains experimentally labelled sites is employed for this purpose and profile bigram occurrences is calculated from position specific scoring matrices of amino acids in the protein sequences. The statistical measures of this work, such as sensitivity, specificity, precision, accuracy, Mathews correlation coefficient and area under ROC curve have been reported to be 0.9642, 0.8973, 0.8253, 0.9193, 0.8330, 0.9306, respectively. CONCLUSIONS The proposed predictor, based on the feature of evolutionary information and support vector machine classifier, has shown great potential to effectively predict phosphoglycerylated and non-phosphoglycerylated lysine residues when compared against the existing predictors. The data and software of this work can be acquired from https://github.com/abelavit/Bigram-PGK.
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Affiliation(s)
- Abel Chandra
- School of Engineering and Physics, Faculty of Science Technology and Environment, University of the South Pacific, Suva, Fiji.
| | - Alok Sharma
- School of Engineering and Physics, Faculty of Science Technology and Environment, University of the South Pacific, Suva, Fiji. .,Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD, 4111, Australia. .,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan. .,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan. .,CREST, JST, Tokyo, 102-8666, Japan.
| | - Abdollah Dehzangi
- Department of Computer Science, Morgan State University, Baltimore, MD, USA
| | - Daichi Shigemizu
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,CREST, JST, Tokyo, 102-8666, Japan.,Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,CREST, JST, Tokyo, 102-8666, Japan.,Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 108-8639, Japan
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Xu X, Cao X, Yang J, Chen L, Liu B, Liu T, Jin Q. Proteome-Wide Identification of Lysine Propionylation in the Conidial and Mycelial Stages of Trichophyton rubrum. Front Microbiol 2019; 10:2613. [PMID: 31798556 PMCID: PMC6861857 DOI: 10.3389/fmicb.2019.02613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/28/2019] [Indexed: 01/05/2023] Open
Abstract
Posttranslational modifications (PTMs) exist in a wide variety of organisms and play key roles in regulating various essential biological processes. Lysine propionylation is a newly discovered PTM that has rarely been identified in fungi. Trichophyton rubrum (T. rubrum) is one of the most common fungal pathogens in the world and has been studied as an important model organism of anthropic pathogenic filamentous fungi. In this study, we performed a proteome-wide propionylation analysis in the conidial and mycelial stages of T. rubrum. A total of 157 propionylated sites on 115 proteins were identified, and the high confidence of propionylation identification was validated by parallel reaction monitoring (PRM) assay. The results show that the propionylated proteins were mostly involved in various metabolic pathways. Histones and 15 pathogenicity-related proteins were also targets for propionylation modification, suggesting their roles in epigenetic regulation and pathogenicity. A comparison of the conidial and mycelial stages revealed that most propionylated proteins and sites were growth-stage specific and independent of protein abundance. Based on the function classifications, the propionylated proteins had a similar distribution in both stages; however, some differences were also identified. Furthermore, our results show that the concentration of propionyl-CoA had a significant influence on the propionylation level. In addition to the acetylation, succinylation and propionylation identified in T. rubrum, 26 other PTMs were also found to exist in this fungus. Overall, our study provides the first global propionylation profile of a pathogenic fungus. These results would be a foundation for further research on the regulation mechanism of propionylation in T. rubrum, which will enhance our understanding of the physiological features of T. rubrum and provide some clues for the exploration of improved therapies to treat this medically important fungus.
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Affiliation(s)
- Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Liu S, Liu G, Cheng P, Xue C, Zhou Y, Chen X, Ye L, Qiao Z, Zhang T, Gong Z. Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice. RICE (NEW YORK, N.Y.) 2019; 12:86. [PMID: 31776817 PMCID: PMC6881504 DOI: 10.1186/s12284-019-0342-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice. MAIN BODY In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties. CONCLUSION Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.
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Affiliation(s)
- Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Peifeng Cheng
- Suzhou Academy of Agricultural Sciences, North of Wangting Town, Suzhou, 215128, China
| | - Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Xu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Lu Ye
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhongying Qiao
- Suzhou Academy of Agricultural Sciences, North of Wangting Town, Suzhou, 215128, China.
| | - Tao Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety / Key Laboratory of Plant Functional Genomics, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
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Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria. Int J Mol Sci 2019; 20:ijms20194792. [PMID: 31561603 PMCID: PMC6801645 DOI: 10.3390/ijms20194792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.
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Ringel AE, Tucker SA, Haigis MC. Chemical and Physiological Features of Mitochondrial Acylation. Mol Cell 2019; 72:610-624. [PMID: 30444998 DOI: 10.1016/j.molcel.2018.10.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/15/2018] [Accepted: 10/15/2018] [Indexed: 01/09/2023]
Abstract
Growing appreciation of the diversity of post-translational modifications (PTMs) in the mitochondria necessitates reevaluation of the roles these modifications play in both health and disease. Compared to the cytosol and nucleus, the mitochondrial proteome is highly acylated, and remodeling of the mitochondrial "acylome" is a key adaptive mechanism that regulates fundamental aspects of mitochondrial biology. It is clear that we need to understand the underlying chemistry that regulates mitochondrial acylation, as well as how chemical properties of the acyl chain impact biological functions. Here, we dissect the sources of PTMs in the mitochondria, review major mitochondrial pathways that control levels of PTMs, and highlight how sirtuin enzymes respond to the bioenergetic state of the cell via NAD+ availability to regulate mitochondrial biology. By providing a framework connecting the chemistry of these modifications, their biochemical consequences, and the pathways that regulate the levels of acyl PTMs, we will gain a deeper understanding of the physiological significance of mitochondrial acylation and its role in mitochondrial adaptation.
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Affiliation(s)
- Alison E Ringel
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Sarah A Tucker
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA.
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Chandra AA, Sharma A, Dehzangi A, Tsunoda T. EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction. BMC Genomics 2019; 19:984. [PMID: 30999859 PMCID: PMC7402405 DOI: 10.1186/s12864-018-5383-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/17/2018] [Indexed: 01/21/2023] Open
Abstract
Background Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. In the recent times, there has been many reported PTMs. Out of the many modifications, phosphoglycerylation has become particularly the subject of interest. The experimental procedure for identification of phosphoglycerylated residues continues to be an expensive, inefficient and time-consuming effort, even with a large number of proteins that are sequenced in the post-genomic period. Computational methods are therefore being anticipated in order to effectively predict phosphoglycerylated lysines. Even though there are predictors available, the ability to detect phosphoglycerylated lysine residues still remains inadequate. Results We have introduced a new predictor in this paper named EvolStruct-Phogly that uses structural and evolutionary information relating to amino acids to predict phosphoglycerylated lysine residues. Benchmarked data is employed containing experimentally identified phosphoglycerylated and non-phosphoglycerylated lysines. We have then extracted the three structural information which are accessible surface area of amino acids, backbone torsion angles, amino acid’s local structure conformations and profile bigrams of position-specific scoring matrices. Conclusion EvolStruct-Phogly showed a noteworthy improvement in regards to the performance when compared with the previous predictors. The performance metrics obtained are as follows: sensitivity 0.7744, specificity 0.8533, precision 0.7368, accuracy 0.8275, and Mathews correlation coefficient of 0.6242. The software package and data of this work can be obtained from https://github.com/abelavit/EvolStruct-Phogly or www.alok-ai-lab.com
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Affiliation(s)
| | - Alok Sharma
- School of Engineering & Physics, University of the South Pacific, Suva, Fiji. .,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia. .,CREST, JST, Tokyo, Japan.
| | - Abdollah Dehzangi
- Department of Computer Science, Morgan State University, Baltimore, MD, USA
| | - Tatushiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,CREST, JST, Tokyo, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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Nandi SK, Rakete S, Nahomi RB, Michel C, Dunbar A, Fritz KS, Nagaraj RH. Succinylation Is a Gain-of-Function Modification in Human Lens αB-Crystallin. Biochemistry 2019; 58:1260-1274. [PMID: 30758948 DOI: 10.1021/acs.biochem.8b01053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acylation of lysine residues is a common post-translational modification of cellular proteins. Here, we show that lysine succinylation, a type of acylation, occurs in human lens proteins. All of the major crystallins exhibited Nε-succinyllysine (SuccK) residues. Quantification of SuccK in human lens proteins (from donors between the ages of 20 and 73 years) by LC-MS/MS showed a range between 1.2 and 14.3 pmol/mg lens protein. The total SuccK levels were slightly reduced in aged lenses (age > 60 years) relative to young lenses (age < 30 years). Immunohistochemical analyses revealed that SuccK was present in epithelium and fiber cells. Western blotting and immunoprecipitation experiments revealed that SuccK is particularly prominent in αB-crystallin, and succinylation in vitro revealed that αB-crystallin is more prone to succinylation than αA-crystallin. Mass spectrometric analyses showed succinylation at K72, K90, K92, K166, K175, and potentially K174 in human lens αB-crystallin. We detected succinylation at K72, K82, K90, K92, K103, K121, K150, K166, K175, and potentially K174 by mass spectrometry in mildly succinylated αB-crystallin. Mild succinylation improved the chaperone activity of αB-crystallin along with minor perturbation in tertiary and quaternary structure of the protein. These observations imply that succinylation is beneficial to αB-crystallin by improving its chaperone activity with only mild conformational alterations.
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50
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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