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Fu JY, Huang SJ, Wang BL, Yin JH, Chen CY, Xu JB, Chen YL, Xu S, Dong T, Zhou HN, Ma XY, Pu YP, Li H, Yang XJ, Xie LS, Wang ZJ, Luo Q, Shao YX, Ye L, Zong ZR, Wei XD, Xiao WW, Niu ST, Liu YM, Xu HP, Yu CQ, Duan SZ, Zheng LY. Lysine acetyltransferase 6A maintains CD4 + T cell response via epigenetic reprogramming of glucose metabolism in autoimmunity. Cell Metab 2024; 36:557-574.e10. [PMID: 38237601 DOI: 10.1016/j.cmet.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Augmented CD4+ T cell response in autoimmunity is characterized by extensive metabolic reprogramming. However, the epigenetic molecule that drives the metabolic adaptation of CD4+ T cells remains largely unknown. Here, we show that lysine acetyltransferase 6A (KAT6A), an epigenetic modulator that is clinically associated with autoimmunity, orchestrates the metabolic reprogramming of glucose in CD4+ T cells. KAT6A is required for the proliferation and differentiation of proinflammatory CD4+ T cell subsets in vitro, and mice with KAT6A-deficient CD4+ T cells are less susceptible to experimental autoimmune encephalomyelitis and colitis. Mechanistically, KAT6A orchestrates the abundance of histone acetylation at the chromatin where several glycolytic genes are located, thus affecting glucose metabolic reprogramming and subsequent CD4+ T cell responses. Treatment with KAT6A small-molecule inhibitors in mouse models shows high therapeutic value for targeting KAT6A in autoimmunity. Our study provides novel insights into the epigenetic programming of immunometabolism and suggests potential therapeutic targets for patients with autoimmunity.
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Affiliation(s)
- Jia-Yao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Shi-Jia Huang
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Bao-Li Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Jun-Hao Yin
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Chang-Yu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Jia-Bao Xu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yan-Lin Chen
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Department of Neurosurgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Shuo Xu
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310000, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Ting Dong
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Hao-Nan Zhou
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Xin-Yi Ma
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yi-Ping Pu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Hui Li
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Xiu-Juan Yang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Li-Song Xie
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Zhi-Jun Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Qi Luo
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yan-Xiong Shao
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Lei Ye
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Zi-Rui Zong
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Xin-Di Wei
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Wan-Wen Xiao
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Shu-Tong Niu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yi-Ming Liu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - He-Ping Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Science, Westlake University, Hangzhou 310024, China
| | - Chuang-Qi Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310000, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China.
| | - Ling-Yan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China.
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Jia K, Yang M, Liu X, Zhang Q, Cao G, Ge F, Zhao J. Deciphering the structure, function, and mechanism of lysine acetyltransferase cGNAT2 in cyanobacteria. Plant Physiol 2024; 194:634-661. [PMID: 37770070 DOI: 10.1093/plphys/kiad509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023]
Abstract
Lysine acetylation is a conserved regulatory posttranslational protein modification that is performed by lysine acetyltransferases (KATs). By catalyzing the transfer of acetyl groups to substrate proteins, KATs play critical regulatory roles in all domains of life; however, no KATs have yet been identified in cyanobacteria. Here, we tested all predicted KATs in the cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) and demonstrated that A1596, which we named cyanobacterial Gcn5-related N-acetyltransferase (cGNAT2), can catalyze lysine acetylation in vivo and in vitro. Eight amino acid residues were identified as the key residues in the putative active site of cGNAT2, as indicated by structural simulation and site-directed mutagenesis. The loss of cGNAT2 altered both growth and photosynthetic electron transport in Syn7002. In addition, quantitative analysis of the lysine acetylome identified 548 endogenous substrates of cGNAT2 in Syn7002. We further demonstrated that cGNAT2 can acetylate NAD(P)H dehydrogenase J (NdhJ) in vivo and in vitro, with the inability to acetylate K89 residues, thus decreasing NdhJ activity and affecting both growth and electron transport in Syn7002. In summary, this study identified a KAT in cyanobacteria and revealed that cGNAT2 regulates growth and photosynthesis in Syn7002 through an acetylation-mediated mechanism.
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Affiliation(s)
- Kun Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Qi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoxiang Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ. Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli. mBio 2018; 9:e01905-18. [PMID: 30352934 PMCID: PMC6199490 DOI: 10.1128/mbio.01905-18] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Posttranslational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.IMPORTANCENε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.
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Affiliation(s)
- David G Christensen
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jackson T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | | | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
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