1
|
Ren C, Chen L, Bai Y, Hou C, Li X, Schroyen M, Zhang D. Comparative effects of phosphorylation and acetylation on glycolysis and myofibrillar proteins degradation in postmortem muscle. Int J Biol Macromol 2024; 257:128567. [PMID: 38061521 DOI: 10.1016/j.ijbiomac.2023.128567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The study investigated the different effects between protein phosphorylation and acetylation on glycolytic enzyme activity and myofibrillar protein degradation. Lamb longissimus thoracis lumborum muscles were homogenized and then inhibitors were added for incubation at 4 °C. Phosphatase inhibitor was added to produce a high phosphorylation level (PI group) and lysine deacetylase inhibitor was added to produce a high acetylation level (DI group). The lactate and ATP content in the PI group was inhibited compared with that in the DI group (P < 0.05). Phosphofructokinase (PFK) activity was negatively related with the phosphorylation level and was positively related with the acetylation level in the DI group (P < 0.05). The degradation of troponin T and desmin of the DI group were restrained when compared to that in the PI group (P < 0.05). Compared with initial PFK and desmin, the simulation of phosphorylation and acetylation of PFK and desmin showed different electrostatic potential at the surface and a more unstable structure. The phosphorylation level of the DI group was increased, suggesting that the changes of protein acetylation altered protein phosphorylation. In conclusion, compared with protein phosphorylation, protein acetylation had a greater effect on promoting glycolysis and inhibiting protein degradation.
Collapse
Affiliation(s)
- Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Li Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Yuqiang Bai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| |
Collapse
|
2
|
Chen G, Bao B, Cheng Y, Tian M, Song J, Zheng L, Tong Q. Acetyl-CoA metabolism as a therapeutic target for cancer. Biomed Pharmacother 2023; 168:115741. [PMID: 37864899 DOI: 10.1016/j.biopha.2023.115741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023] Open
Abstract
Acetyl-coenzyme A (acetyl-CoA), an essential metabolite, not only takes part in numerous intracellular metabolic processes, powers the tricarboxylic acid cycle, serves as a key hub for the biosynthesis of fatty acids and isoprenoids, but also serves as a signaling substrate for acetylation reactions in post-translational modification of proteins, which is crucial for the epigenetic inheritance of cells. Acetyl-CoA links lipid metabolism with histone acetylation to create a more intricate regulatory system that affects the growth, aggressiveness, and drug resistance of malignancies such as glioblastoma, breast cancer, and hepatocellular carcinoma. These fascinating advances in the knowledge of acetyl-CoA metabolism during carcinogenesis and normal physiology have raised interest regarding its modulation in malignancies. In this review, we provide an overview of the regulation and cancer relevance of main metabolic pathways in which acetyl-CoA participates. We also summarize the role of acetyl-CoA in the metabolic reprogramming and stress regulation of cancer cells, as well as medical application of inhibitors targeting its dysregulation in therapeutic intervention of cancers.
Collapse
Affiliation(s)
- Guo Chen
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Banghe Bao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Yang Cheng
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Minxiu Tian
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Jiyu Song
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
| |
Collapse
|
3
|
Li XY, Yu JT, Dong YH, Shen XY, Hou R, Xie MM, Wei J, Hu XW, Dong ZH, Shan RR, Jin J, Shao W, Meng XM. Protein acetylation and related potential therapeutic strategies in kidney disease. Pharmacol Res 2023; 197:106950. [PMID: 37820854 DOI: 10.1016/j.phrs.2023.106950] [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: 08/03/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Kidney disease can be caused by various internal and external factors that have led to a continual increase in global deaths. Current treatment methods can alleviate but do not markedly prevent disease development. Further research on kidney disease has revealed the crucial function of epigenetics, especially acetylation, in the pathology and physiology of the kidney. Histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyllysine readers jointly regulate acetylation, thus affecting kidney physiological homoeostasis. Recent studies have shown that acetylation improves mechanisms and pathways involved in various types of nephropathy. The discovery and application of novel inhibitors and activators have further confirmed the important role of acetylation. In this review, we provide insights into the physiological process of acetylation and summarise its specific mechanisms and potential therapeutic effects on renal pathology.
Collapse
Affiliation(s)
- Xiang-Yu Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ju-Tao Yu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yu-Hang Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Xiao-Yu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Rui Hou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Man-Man Xie
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Jie Wei
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei 230601, Anhui, China
| | - Xiao-Wei Hu
- Department of Clinical Pharmacy, Anhui Provincial Children's Hospital, Hefei 230051, China
| | - Ze-Hui Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Run-Run Shan
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Juan Jin
- Research Center for Translational Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China.
| |
Collapse
|
4
|
Jiang N, Li W, Jiang S, Xie M, Liu R. Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects. Biomed Pharmacother 2023; 167:115519. [PMID: 37729729 DOI: 10.1016/j.biopha.2023.115519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023] Open
Abstract
Protein acetylation modifications play a central and pivotal role in a myriad of biological processes, spanning cellular metabolism, proliferation, differentiation, apoptosis, and beyond, by effectively reshaping protein structure and function. The metabolic state of cells is intricately connected to epigenetic modifications, which in turn influence chromatin status and gene expression patterns. Notably, pathological alterations in protein acetylation modifications are frequently observed in diseases such as metabolic syndrome, cardiovascular disorders, and cancer. Such abnormalities can result in altered protein properties and loss of function, which are closely associated with developing and progressing related diseases. In recent years, the advancement of precision medicine has highlighted the potential value of protein acetylation in disease diagnosis, treatment, and prevention. This review includes provocative and thought-provoking papers outlining recent breakthroughs in acetylation modifications as they relate to cardiovascular disease, mitochondrial metabolic regulation, liver health, neurological health, obesity, diabetes, and cancer. Additionally, it covers the molecular mechanisms and research challenges in understanding the role of acetylation in disease regulation. By summarizing novel targets and prognostic markers for the treatment of related diseases, we aim to contribute to the field. Furthermore, we discuss current hot topics in acetylation research related to health regulation, including N4-acetylcytidine and liquid-liquid phase separation. The primary objective of this review is to provide insights into the functional diversity and underlying mechanisms by which acetylation regulates proteins in disease contexts.
Collapse
Affiliation(s)
- Nan Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Wenyong Li
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Shuanglin Jiang
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Ming Xie
- North China Petroleum Bureau General Hospital, Renqiu 062550, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| |
Collapse
|
5
|
Langousis G, Sanchez J, Kempf G, Matthias P. Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol Biol 2023; 2589:467-480. [PMID: 36255643 DOI: 10.1007/978-1-0716-2788-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain. HDAC6 is involved in various biological processes, such as cell motility or stress responses, and has been implicated in pathologies ranging from cancer to neurodegeneration. Due to this broad range of functions, there has been considerable interest in developing HDAC6-specific small molecule inhibitors, several of which are already available. The crystal structure of the tandem catalytic domains of zebrafish HDAC6 has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains. Further dissection of the biochemical properties of HDAC6 and the development of novel inhibitors will benefit from being able to routinely express high-quality protein. We present here our optimized protocol for expression and crystallization of the zebrafish tandem catalytic domains.
Collapse
Affiliation(s)
| | - Jacint Sanchez
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
6
|
Donnarumma F, Tucci V, Ambrosino C, Altucci L, Carafa V. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Clin Epigenetics 2022; 14:182. [PMID: 36539894 PMCID: PMC9769039 DOI: 10.1186/s13148-022-01402-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Chromatin structural organization, gene expression and proteostasis are intricately regulated in a wide range of biological processes, both physiological and pathological. Protein acetylation, a major post-translational modification, is tightly involved in interconnected biological networks, modulating the activation of gene transcription and protein action in cells. A very large number of studies describe the pivotal role of the so-called acetylome (accounting for more than 80% of the human proteome) in orchestrating different pathways in response to stimuli and triggering severe diseases, including cancer. NAA60/NatF (N-terminal acetyltransferase F), also named HAT4 (histone acetyltransferase type B protein 4), is a newly discovered acetyltransferase in humans modifying N-termini of transmembrane proteins starting with M-K/M-A/M-V/M-M residues and is also thought to modify lysine residues of histone H4. Because of its enzymatic features and unusual cell localization on the Golgi membrane, NAA60 is an intriguing acetyltransferase that warrants biochemical and clinical investigation. Although it is still poorly studied, this review summarizes current findings concerning the structural hallmarks and biological role of this novel targetable epigenetic enzyme.
Collapse
Affiliation(s)
- Federica Donnarumma
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy
| | - Valeria Tucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Concetta Ambrosino
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.47422.370000 0001 0724 3038Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Lucia Altucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Vincenzo Carafa
- grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| |
Collapse
|
7
|
Bowker Z, Goldstein S, Breitbart H. Protein acetylation protects sperm from spontaneous acrosome reaction. Theriogenology 2022; 191:231-238. [PMID: 35998406 DOI: 10.1016/j.theriogenology.2022.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
In order to penetrate the egg, spermatozoa must undergo the acrosome reaction in close proximity to the egg. This process can take place only after a series of biochemical changes in the sperm, collectively termed capacitation, occur in the female reproductive tract. Sperm cells can undergo spontaneous-acrosome reaction(sAR) before reaching the vicinity of the egg, preventing successful fertilization. Several mechanisms were shown to protect sperm from undergoing sAR, and all of them are involved in proper capacitation. Here, we describe the involvement of protein acetylation in the mechanism that protects bovine spermatozoa from sAR. Incubation of bovine sperm under non-capacitation conditions revealed a strong increase in sAR that was significantly reduced in the presence of deacetylase inhibitors. Protein kinase A (PKA) is an essential key enzyme in sperm capacitation, and its inhibition results in high sAR. The reduction in sAR by hyperacetylation was independent of PKA activity. We previously demonstrated that calmodulin-kinase II (CaMKII) activity protects sperm from sAR, and here we show that its activity is essential for reduction in sAR by hyperacetylation. We further show that the 'exchange protein directly activated by Camp' (EPAC) mediates both protein lysine acetylation and the reduced rate of sAR caused by hyperacetylation. In conclusion, these results suggest a PKA-independent and EPAC-CaMKII dependent hyperacetylation mechanism that protects sperm from sAR.
Collapse
Affiliation(s)
- Z Bowker
- The Mina & Everard Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - S Goldstein
- The Mina & Everard Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - H Breitbart
- The Mina & Everard Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
| |
Collapse
|
8
|
Xu Q, Wang Y, Chen Z, Yue Y, Huang H, Wu B, Liu Y, Zhou DX, Zhao Y. ROS-stimulated Protein Lysine Acetylation Is Required for Crown Root Development in Rice. J Adv Res 2022:S2090-1232(22)00164-3. [PMID: 35908726 DOI: 10.1016/j.jare.2022.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/27/2022] [Accepted: 07/23/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION As signal molecules in aerobic organisms, locally accumulated ROS have been reported to balance cell division and differentiation in the root meristem. Protein posttranslational modifications such as lysine acetylation play critical roles in controlling a variety of cellular processes. However, the mechanism by which ROS regulate root development is unknown. In addition, how protein lysine acetylation is regulated and whether cellular ROS levels affect protein lysine acetylation remain unclear. OBJECTIVES We aimed to elucidate the relationship between ROS and protein acetylation by exploring a rice mutant plant that displays a decreased level of ROS in postembryonic crown root (CR) cells and severe defects in CR development. METHODS First, proteomic analysis was used to find candidate proteins responsible for the decrease of ROS detected in the wox11 mutant. Then, biochemical, molecular, and genetic analyses were used to study WOX11-regulated genes involved in ROS homeostasis. Finally, acetylproteomic analysis of wild type and wox11 roots treated with or without potassium iodide (KI) and peroxide (H2O2) were used to study the effects of ROS on protein acetylation in rice CR cells. RESULTS We demonstrated that WOX11 was required to maintain ROS homeostasis by upregulating peroxidase genes in the crown root meristem. Acetylproteomic analysis revealed that WOX11-dependent peroxide (H2O2) levels in CR cells promoted lysine acetylation of many non-histone proteins enriched for nitrogen metabolism and peptide/protein synthesis pathways. Further analysis revealed that the redox state affected histone deacetylases (HDACs) activity, which was likely related to the high levels of protein lysine acetylation in CR cells. CONCLUSION WOX11-controlled ROS level in CR meristem cells is required for protein lysine acetylation which represents a mechanism of ROS-promoted CR development in rice.
Collapse
|
9
|
Lee K, Park SH, Lee JH. Selective detection of protein acetylation by NMR spectroscopy. J Magn Reson 2022; 337:107169. [PMID: 35255256 DOI: 10.1016/j.jmr.2022.107169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
Selective detection of biomolecules and their modifications in cells is essential for understanding cell functions and diseases. We have developed an NMR pulse sequence, Ac-FIND (Acetylation-FIltered aNd eDited), which uses isotope editing/filtering techniques for selective detection of protein acetylation. Acetylation of the N-terminus and lysine side chains by N-succinimidyl acetate was selectively observed for intrinsically disordered α-synuclein and well-ordered ubiquitin. Furthermore, when nonacetylated 13C/15N-enriched α-synuclein was introduced into live HEK293 cells, intracellular N-terminal acetylation of α-synuclein was detected by the appearance of a single peak using Ac-FIND. This work demonstrates the utility of NMR to detect a specific protein modification both in vitro and in live cells.
Collapse
Affiliation(s)
- Kyungryun Lee
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, South Korea.
| |
Collapse
|
10
|
Liu X, Zhang Y, Deng Y, Yang L, Ou W, Xie M, Ding L, Jiang C, Yu H, Li Q, Li T. Mitochondrial protein hyperacetylation underpins heart failure with preserved ejection fraction in mice. J Mol Cell Cardiol 2022; 165:76-85. [PMID: 34998831 DOI: 10.1016/j.yjmcc.2021.12.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/03/2021] [Accepted: 12/31/2021] [Indexed: 02/08/2023]
Abstract
Over 50% of patients with heart failure have preserved ejection fraction (HFpEF), rather than reduced ejection fraction (HFrEF). The prevalence of HFpEF continues to increase, while the pathogenic mechanisms underlying HFpEF remain largely elusive and evidence-based therapies are still lacking. This study was designed to investigate the metabolic signature of HFpEF and test the potential therapeutic intervention in a mouse model. By utilizing a "3-Hit" HFpEF mouse model, we observed a global protein hyperacetylation in the HFpEF hearts as compared to the pressure overload-induced HFrEF and adult/aged non-heart failure (NHF) hearts. Acetylome analysis identified that a large proportion of the hyperacetylated proteins (74%) specific to the HFpEF hearts are in mitochondria, and enriched in tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and fatty acid oxidation. Further study showed that the elevated protein acetylation in the HFpEF hearts was correlated with reduced NAD+/NADH ratio, impaired mitochondrial function, and depleted TCA cycle metabolites. Normalization of NAD+/NADH ratio by supplementation of nicotinamide riboside (NR) for 30 days downregulated the acetylation level, improved mitochondrial function and ameliorated HFpEF phenotypes. Therefore, our study identified a distinct protein acetylation pattern in the HFpEF hearts, and proposed NR as a promising agent in lowering acetylation and mitigating HFpEF phenotypes in mice.
Collapse
Affiliation(s)
- Xin Liu
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yabing Zhang
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yan Deng
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lin Yang
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Department of Pharmacy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Ou
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Maodi Xie
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lin Ding
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chunling Jiang
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hai Yu
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qian Li
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Tao Li
- Department of Anesthesiology, Laboratory of Mitochondria and Metabolism, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China; Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital of Sichuan University, Chengdu 610041, China.
| |
Collapse
|
11
|
Tan YS, Wang L, Wang YY, He QE, Liu ZH, Zhu Z, Song K, Li BZ, Yuan YJ. Protein acetylation regulates xylose metabolism during adaptation of Saccharomyces cerevisiae. Biotechnol Biofuels 2021; 14:241. [PMID: 34920742 PMCID: PMC8684234 DOI: 10.1186/s13068-021-02090-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND As the second most abundant polysaccharide in nature, hemicellulose can be degraded to xylose as the feedstock for bioconversion to fuels and chemicals. To enhance xylose conversion, the engineered Saccharomyces cerevisiae with xylose metabolic pathway is usually adapted with xylose as the carbon source in the laboratory. However, the mechanism under the adaptation phenomena of the engineered strain is still unclear. RESULTS In this study, xylose-utilizing S. cerevisiae was constructed and used for the adaptation study. It was found that xylose consumption rate increased 1.24-fold in the second incubation of the yYST12 strain in synthetic complete-xylose medium compared with the first incubation. The study figured out that it was observed at the single-cell level that the stagnation time for xylose utilization was reduced after adaptation with xylose medium in the microfluidic device. Such transient memory of xylose metabolism after adaptation with xylose medium, named "xylose consumption memory", was observed in the strains with both xylose isomerase pathway and xylose reductase and xylitol dehydrogenase pathways. In further, the proteomic acetylation of the strains before and after adaptation was investigated, and it was revealed that H4K5 was one of the most differential acetylation sites related to xylose consumption memory of engineered S. cerevisiae. We tested 8 genes encoding acetylase or deacetylase, and it was found that the knockout of the GCN5 and HPA2 encoding acetylases enhanced the xylose consumption memory. CONCLUSIONS The behavior of xylose consumption memory in engineered S. cerevisiae can be successfully induced with xylose in the adaptation. H4K5Ac and two genes of GCN5 and HPA2 are related to xylose consumption memory of engineered S. cerevisiae during adaptation. This study provides valuable insights into the xylose adaptation of engineered S. cerevisiae.
Collapse
Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Ying Wang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| |
Collapse
|
12
|
Yan J, Nian Y, Zou B, Wu J, Zhou G, Li C. Acetylation inhibition alleviates energy metabolism in muscles of minipigs varying with the type of muscle fibers. Meat Sci 2022; 184:108699. [PMID: 34700176 DOI: 10.1016/j.meatsci.2021.108699] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/31/2021] [Accepted: 10/16/2021] [Indexed: 11/22/2022]
Abstract
In this study, we investigated whether preslaughter chemical-induced acetylation affected postmortem energy metabolism and pork quality. Thirty pigs were randomly assigned to control, acetyltransferase inhibitor (ATi) or deacetyltransferase inhibitor treatments. Serum, trapezius, longissimus lumborum, psoas major, semimembranosus and semitendinosus muscles were taken for analyses. The results indicated that ATi treatment significantly reduced the activities of lactate dehydrogenase and creatine kinase and heat shock protein 70 in serum (P < 0.05). ATi treatment increased ATP and glycogen content, but decreased lactic acid content in trapezius, psoas major and semitendinosus muscles (P < 0.05). A total of 13 acetylated proteins bands were identified and the deacetylation of creatine kinase may play a key role in slowing down the postmortem energy metabolism in ATi-treated group. In addition, ATi treatment reduced the rate of postmortem glycolysis in muscles with higher oxidative but lower glycolytic fibers. These findings provide a new insight into the underlying mechanism on muscle-specific postmortem changes of pork quality.
Collapse
|
13
|
Zhang L, Cao W. Histone deacetylase 3 (HDAC3) as an important epigenetic regulator of kidney diseases. J Mol Med (Berl) 2021; 100:43-51. [PMID: 34698870 DOI: 10.1007/s00109-021-02141-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 12/18/2022]
Abstract
Development and progression of many kidney diseases are substantially influenced by aberrant protein acetylation modifications of gene expression crucial for kidney functions. Histone deacetylase (HDAC) expression alterations are detected from renal samples of patients and animal models of various kidney diseases, and the administrations of HDAC inhibitors display impressive renal protective effects in vitro and in vivo. However, when the expression alterations of multiple HDACs occur, not all the HDACs causally affect the disease onset or progression. Identification of a single HDAC as a disease-causing factor will allow subtype-targeted intervention with less side effect. HDAC3 is a unique HDAC with distinct structural and subcellular distribution features and co-repressor dependency. HDAC3 is required for kidney development and its aberrations actively participate in many pathological processes, such as cancer, cardiovascular diseases, diabetes, and neurodegenerative disorders, and contribute significantly to the pathogenesis of kidney diseases. This review will discuss the recent studies that investigate the critical roles of HDAC3 aberrations in kidney development, renal aging, renal cell carcinoma, renal fibrosis, chronic kidney disease, polycystic kidney disease, glomerular podocyte injury, and diabetic nephropathy. These studies reveal the distinct characters of HDAC3 aberrations that act on different molecules/signaling pathways under various renal pathological conditions, which might shed lights into the epigenetic mechanisms of renal diseases and the potentially therapeutic strategies.
Collapse
Affiliation(s)
- Lijun Zhang
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Wangsen Cao
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China.
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
| |
Collapse
|
14
|
Liu M, Guo L, Fu Y, Huo M, Qi Q, Zhao G. Bacterial protein acetylation and its role in cellular physiology and metabolic regulation. Biotechnol Adv 2021; 53:107842. [PMID: 34624455 DOI: 10.1016/j.biotechadv.2021.107842] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 10/03/2021] [Indexed: 12/28/2022]
Abstract
Protein acetylation is an evolutionarily conserved posttranslational modification. It affects enzyme activity, metabolic flux distribution, and other critical physiological and biochemical processes by altering protein size and charge. Protein acetylation may thus be a promising tool for metabolic regulation to improve target production and conversion efficiency in fermentation. Here we review the role of protein acetylation in bacterial physiology and metabolism and describe applications of protein acetylation in fermentation engineering and strategies for regulating acetylation status. Although protein acetylation has become a hot topic, the regulatory mechanisms have not been fully characterized. We propose future research directions in protein acetylation.
Collapse
Affiliation(s)
- Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Meitong Huo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| |
Collapse
|
15
|
Hu X, Wang D, Sun L, Gao Y, Zhou D, Tong X, Li J, Lin H, Qing Y, Du S, Yang X, Jiang J, Yan G, Wei Z, Wang Q, Zhang J, He L, Wan C. Disturbed mitochondrial acetylation in accordance with the availability of acetyl groups in hepatocellular carcinoma. Mitochondrion 2021; 60:150-9. [PMID: 34375734 DOI: 10.1016/j.mito.2021.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 07/06/2021] [Accepted: 08/05/2021] [Indexed: 12/29/2022]
Abstract
As an essential post-translational modification, acetylation participates in various cellular processes and shows aberrances during tumorigenesis. Owing to its modification substrate, acetyl-CoA, acetylation is postulated as a depot for acetyl groups and evolve to build a connection between epigenetics and metabolism. Here we depict a distinct acetylome atlas of hepatocellular carcinoma from the perspectives of both protein acetylation and acetyl-CoA metabolism. We found that tumor acetylome demonstrated a compartment-dependent alteration that the acetylation level of mitochondrial proteins tended to be decreased while nuclear proteins were highly acetylated. In addition, elevated expression of ATP-citrate synthase (ACLY) was observed in tumors, which would facilitate histone acetylation by transporting mitochondrial acetyl coenzyme A to the nucleus. A hypothetical model of the oncogenic acetylome was proposed that growing demands for histone acetylation in tumor cells would drive the relocalization of acetyl-CoA to the nucleus, which may contribute to the global deacetylation of mitochondrial proteins to support the nuclear acetyl-CoA pool in an ACLY-dependent manner. Our findings are thought-provoking on the potential linkage between epigenetics and metabolism in the progression of tumorigenesis.
Collapse
|
16
|
Jing Z, Gao J, Li J, Niu F, Tian L, Nan P, Sun Y, Xie X, Zhu Y, Zhao Y, Liu F, Zhou L, Sun Y, Zhao X. Acetylation-induced PCK isoenzyme transition promotes metabolic adaption of liver cancer to systemic therapy. Cancer Lett 2021; 519:46-62. [PMID: 34166767 DOI: 10.1016/j.canlet.2021.06.016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 12/24/2022]
Abstract
Sorafenib and lenvatinib are approved first-line targeted therapies for advanced liver cancer, but most patients develop acquired resistance. Herein, we found that sorafenib induced extensive acetylation changes towards a more energetic metabolic phenotype. Metabolic adaptation was mediated via acetylation of the Lys-491 (K491) residue of phosphoenolpyruvate carboxykinase isoform 2 (PCK2) (PCK2-K491) and Lys-473 (K473) residue of PCK1 (PCK1-K473) by the lysine acetyltransferase 8 (KAT8), resulting in isoenzyme transition from cytoplasmic PCK1 to mitochondrial PCK2. KAT8-catalyzed PCK2 acetylation at K491 impeded lysosomal degradation to increase the level of PCK2 in resistant cells. PCK2 inhibition in sorafenib-resistant cells significantly reversed drug resistance in vitro and in vivo. High levels of PCK2 predicted a shorter progression-free survival time in patients who received sorafenib treatment. Therefore, acetylation-induced isoenzyme transition from PCK1 to PCK2 contributes to resistance to systemic therapeutic drugs in liver cancer. PCK2 may be an emerging target for delaying tumor recurrence.
Collapse
Affiliation(s)
- Zongpan Jing
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiajia Gao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jun Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fangfei Niu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lusong Tian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Nan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yan Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiufeng Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ying Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yan Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lanping Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yulin Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Xiaohang Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
17
|
Zúñiga-Muñoz A, García-Niño WR, Carbó R, Navarrete-López LÁ, Buelna-Chontal M. The regulation of protein acetylation influences the redox homeostasis to protect the heart. Life Sci 2021; 277:119599. [PMID: 33989666 DOI: 10.1016/j.lfs.2021.119599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022]
Abstract
The cellular damage caused by redox imbalance is involved in the pathogenesis of many cardiovascular diseases. Besides, redox imbalance is related to the alteration of protein acetylation processes, causing not only chromatin remodeling but also disturbances in so many processes where protein acetylation is involved, such as metabolism and signal transduction. The modulation of acetylases and deacetylases enzymes aids in maintaining the redox homeostasis, avoiding the deleterious cellular effects associated with the dysregulation of protein acetylation. Of note, regulation of protein acetylation has shown protective effects to ameliorate cardiovascular diseases. For instance, HDAC inhibition has been related to inducing cardiac protective effects and it is an interesting approach to the management of cardiovascular diseases. On the other hand, the upregulation of SIRT protein activity has also been implicated in the relief of cardiovascular diseases. This review focuses on the major protein acetylation modulators described, involving pharmacological and bioactive compounds targeting deacetylase and acetylase enzymes contributing to heart protection through redox homeostasis.
Collapse
Affiliation(s)
- Alejandra Zúñiga-Muñoz
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Wylly-Ramsés García-Niño
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Roxana Carbó
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Luis-Ángel Navarrete-López
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Mabel Buelna-Chontal
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico.
| |
Collapse
|
18
|
Saito M, Iestamantavicius V, Hess D, Matthias P. Monitoring Acetylation of the RNA Helicase DDX3X, a Protein Critical for Formation of Stress Granules. Methods Mol Biol 2021; 2209:217-234. [PMID: 33201472 DOI: 10.1007/978-1-0716-0935-4_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stress granules are dynamic structures that assemble in response to various forms of stress, such as heat shock or oxidative stress, among others. We had previously shown that the lysine deacetylase HDAC6 is required for the formation of stress granules, but the substrate important for this function was not known. We recently found that the RNA helicase DDX3X is a novel HDAC6 substrate, which is critical for the formation of stress granules. Through a series of detailed experiments, we showed that, upon stress, DDX3X becomes acetylated in an intrinsically disordered region; this alters its propensity to undergo phase separation and inhibits growth of the stress granules. HDAC6, by deacetylating DDX3X, allows maturation of the stress granules. This work identified acetylation of an RNA helicase as a critical regulator of the stress response. Here, we present methods to analyze the acetylation of DDX3X; these methods can be easily adapted to study the acetylation of other helicases, or other proteins.
Collapse
Affiliation(s)
- Makoto Saito
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
19
|
Zhang Y, Wang S, Zhang L, Zhou F, Zhu K, Zhu Q, Liu Q, Liu Y, Jiang L, Ning G, Bi Y, Zhou L, Wang X. Protein acetylation derepresses Serotonin Synthesis to potentiate Pancreatic Beta-Cell Function through HDAC1-PKA-Tph1 signaling. Am J Cancer Res 2020; 10:7351-7368. [PMID: 32641996 PMCID: PMC7330849 DOI: 10.7150/thno.44459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Rationale: Protein acetylation is tightly linked to transcriptional control and energy metabolism. However, the role of protein acetylation in islet function remains enigmatic. This study aims to determine how protein acetylation controls β-cell function and explore the underlying mechanism. Methods: The gene-expression profiles were analyzed for rat islets in response to two histone deacetylase (HDAC) inhibitors. Insulin secretion, tryptophan hydroxylase 1 (Tph1) expression, and serotonin synthesis of rat islets were detected after HDAC inhibitor treatment both in vivo and ex vivo. β-cell-specific Tph1-overexpressing transgenic rats and β-cell-specific Tph1 knockout mice were constructed to evaluate the role of Tph1 in β-cell function. The deacetylation of PKA in β-cells by HDAC1 was investigated by adenoviral infection, immunoprecipitation, and western blot. Results: Inhibition of HDACs greatly potentiated pancreatic β-cell function and reprogrammed transcriptional landscape of islets. Among the commonly up-regulated genes by two pan-HDAC inhibitors, Tph1 displayed the most prominent change. Specifically, inhibition of HDAC1 and HDAC3 by MS-275 strongly promoted Tph1 expression and endogenous serotonin synthesis in rat islets, concomitantly with enhanced insulin secretory capacity in vivo and ex vivo. β-cell-specific Tph1-overexpressing transgenic rats exhibited improved glucose tolerance and amplified glucose-stimulated insulin secretion. On the contrary, β-cell-specific Tph1 knockout mice displayed glucose intolerance and impaired insulin secretion with aging. Moreover, depletion of Tph1 in β-cells abrogated MS-275-induced insulin hypersecretion. Overexpression of HDAC1, not HDAC3, inhibited Tph1 transcriptional activity and decreased MS-275-stimulated Tph1 expression. Mechanistically, HDAC1 deacetylated PKA catalytic subunit and decreased its activity, resulting in Tph1 transcriptional repression. The acetylation mimetic K62Q mutant of PKA increased its catalytic activity. HDAC1 inhibition exerted a synergistic effect with cAMP/PKA signal on Tph1 expression. Conclusions: The present findings highlight a novel role of HDAC1-PKA-Tph1 signaling in governing β-cell functional compensation by derepressing serotonin synthesis.
Collapse
|
20
|
Bhatt AN, Rai Y, Verma A, Pandey S, Kaushik K, Parmar VS, Arya A, Prasad AK, Dwarakanath BS. Non-Enzymatic Protein Acetylation by 7-Acetoxy-4-Methylcoumarin: Implications in Protein Biochemistry. Protein Pept Lett 2020; 27:736-743. [PMID: 32133945 DOI: 10.2174/0929866527666200305143016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/23/2019] [Accepted: 12/29/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND The semi-synthetic acetoxycoumarins are known to acetylate proteins using novel enzymatic Calreticulin Transacetylase (CRTAase) system in cells. However, the nonenzymatic protein acetylation by polyphenolic acetates is not known. OBJECTIVE To investigate the ability of 7-acetoxy-4-methyl coumarin (7-AMC) to acetylate proteins non-enzymatically in the test tube. METHODS We incubated 7-AMC with BSA and analyzed the protein acetylation using Western blot technique. Further, BSA induced biophysical changes in the spectroscopic properties of 7-AMC was analyzed using Fluorescence spectroscopy. RESULTS Using pan anti-acetyl lysine antibody, herein we demonstrate that 7-AMC acetylates Bovine Serum Albumin (BSA) in time and concentration dependent manner in the absence of any enzyme. 7-AMC is a relatively less fluorescent molecule compared to the parental compound, 7- hydroxy-4-methylcoumarin (7-HMC), however the fluorescence of 7-AMC increased by two fold on incubation with BSA, depending on the time of incubation and concentration of BSA. Analysis of the reaction mixture of 7-AMC and BSA after filtration revealed that the increased fluorescence is associated with the compound of lower molecular weight in the filtrate and not residual BSA, suggesting that the less fluorescent 7-AMC undergoes self-hydrolysis in the presence of protein to give highly fluorescent parental molecule 7-HMC and acetate ion in polar solvent (phosphate buffered saline, PBS). The protein augmented conversion of 7-AMC to 7-HMC was found to be linearly related to the protein concentration. CONCLUSION Thus protein acetylation induced by 7-AMC could also be non-enzymatic in nature and this molecule can be exploited for quantification of proteins.
Collapse
Affiliation(s)
- Anant Narayan Bhatt
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Majumdar Marg, Timarpur, Delhi, India
| | - Yogesh Rai
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Majumdar Marg, Timarpur, Delhi, India
| | - Amit Verma
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Majumdar Marg, Timarpur, Delhi, India
| | - Sanjay Pandey
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Majumdar Marg, Timarpur, Delhi, India
| | - Kumar Kaushik
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, New York City, NY, United States
| | - Virinder S Parmar
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, New York City, NY, United States
| | - Anu Arya
- V.P. Chest Institute, Delhi, India
| | - Ashok K Prasad
- Deparment of Chemistry, University of Delhi, Delhi, India
| | - Bilikere S Dwarakanath
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Majumdar Marg, Timarpur, Delhi, India
| |
Collapse
|
21
|
Schreiber KJ, Lewis JD. Protein Acetylation in Pathogen Virulence and Host Defense: In Vitro Detection of Protein Acetylation by Radiolabeled Acetyl Coenzyme A. Methods Mol Biol 2020; 1991:23-32. [PMID: 31041759 DOI: 10.1007/978-1-4939-9458-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein acetylation has emerged as a common modification that modulates multiple aspects of protein function, including localization, stability, and protein-protein interactions. It is increasingly evident that protein acetylation significantly impacts the outcome of host-microbe interactions. In order to characterize novel putative acetyltransferase enzymes and their substrates, we describe a simple protocol for the detection of acetyltransferase activity in vitro. Purified proteins are incubated with 14C-acetyl CoA and separated electrophoretically, and acetylated proteins are detected by phosphorimaging or autoradiography.
Collapse
Affiliation(s)
- Karl J Schreiber
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA. .,Plant Gene Expression Center, United States Department of Agriculture, Albany, CA, USA.
| |
Collapse
|
22
|
Ferreira LL, Cervantes M, Froufe HJC, Egas C, Cunha-Oliveira T, Sassone-Corsi P, Oliveira PJ. Doxorubicin persistently rewires cardiac circadian homeostasis in mice. Arch Toxicol 2019; 94:257-271. [PMID: 31768571 DOI: 10.1007/s00204-019-02626-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022]
Abstract
Circadian rhythms disruption can be the cause of chronic diseases. External cues, including therapeutic drugs, have been shown to modulate peripheral-circadian clocks. Since anthracycline cardiotoxicity is associated with loss of mitochondrial function and metabolic remodeling, we investigated whether the energetic failure induced by sub-chronic doxorubicin (DOX) treatment in juvenile mice was associated with persistent disruption of circadian regulators. Juvenile C57BL/6J male mice were subjected to a sub-chronic DOX treatment (4 weekly injections of 5 mg/kg DOX) and several cardiac parameters, as well as circadian-gene expression and acetylation patterns, were analyzed after 6 weeks of recovery time. Complementary experiments were performed with Mouse Embryonic Fibroblasts (MEFs) and Human Embryonic Kidney 293 cells. DOX-treated juvenile mice showed cardiotoxicity markers and persistent alterations of transcriptional- and signaling cardiac circadian homeostasis. The results showed a delayed influence of DOX on gene expression, accompanied by changes in SIRT1-mediated cyclic deacetylation. The mechanism behind DOX interference with the circadian clock was further studied in vitro, in which were observed alterations of circadian-gene expression and increased BMAL1 SIRT1-mediated deacetylation. In conclusion, DOX treatment in juvenile mice resulted in disruption of oscillatory molecular mechanisms including gene expression and acetylation profiles.
Collapse
Affiliation(s)
- Luciana L Ferreira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal
| | - Marlene Cervantes
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Hugo J C Froufe
- Next Generation Sequencing Unit, Biocant, Biocant Park, Núcleo 04, Lote 8, Cantanhede, Portugal
| | - Conceição Egas
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal.,Next Generation Sequencing Unit, Biocant, Biocant Park, Núcleo 04, Lote 8, Cantanhede, Portugal
| | - Teresa Cunha-Oliveira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Paulo J Oliveira
- Mitochondrial Toxicology and Experimental Therapeutics Laboratory (MitoXT), CNC, Center for Neuroscience and Cell Biology, University of Coimbra, UC Biotech Building (Lote 8A), Biocant Park, 3060-197, Cantanhede, Portugal. .,Institute for Interdisciplinary Research (I.I.I.), University of Coimbra, Coimbra, Portugal.
| |
Collapse
|
23
|
Laskowska E, Kuczyńska-Wiśnik D. New insight into the mechanisms protecting bacteria during desiccation. Curr Genet 2019; 66:313-318. [PMID: 31559453 PMCID: PMC7069898 DOI: 10.1007/s00294-019-01036-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/29/2022]
Abstract
Desiccation is a common stress that bacteria face in the natural environment, and thus, they have developed a variety of protective mechanisms to mitigate the damage caused by water loss. The formation of biofilms and the accumulation of trehalose and sporulation are well-known strategies used by bacteria to survive desiccation. Other mechanisms, including intrinsically disordered proteins and the anti-glycation defence, have been mainly studied in eukaryotic cells, and their role in bacteria remains unclear. We have recently shown that the impairment of trehalose synthesis results in higher glucose availability, leading to the accumulation of acetyl phosphate and enhanced protein acetylation, which in turn stimulates protein aggregation. In the absence of trehalose synthesis, excess glucose may stimulate non-enzymatic glycosylation and the formation of advanced glycation end products (AGEs) bound to proteins. Therefore, we propose that trehalose may prevent protein damage, not only as a chemical chaperone but also as a metabolite that indirectly counteracts detrimental protein acetylation and glycation.
Collapse
Affiliation(s)
- Ewa Laskowska
- Faculty of Biology, Department of General and Medical Biochemistry, University of Gdansk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Dorota Kuczyńska-Wiśnik
- Faculty of Biology, Department of General and Medical Biochemistry, University of Gdansk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| |
Collapse
|
24
|
Storder J, Renard P, Arnould T. Update on the role of Sirtuin 3 in cell differentiation: A major metabolic target that can be pharmacologically controlled. Biochem Pharmacol 2019; 169:113621. [PMID: 31472127 DOI: 10.1016/j.bcp.2019.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023]
Abstract
Cell differentiation is a fundamental biological event in which a precursor stem cell is turning into a specialized somatic cell. It is thus crucial for the development, tissue turnover and regeneration in mammals. Among the numerous changes taking place in a cell during a differentiation programme, the biology of mitochondria, the central organelle mainly responsible for energy homeostasis and stress adaptation, is deeply modified. These modifications are now well recognized as taking an active part to the completion of the differentiation programme. Indeed, mitochondrial biogenesis and metabolic shift are observed during cell differentiation, adapting many syntheses, calcium homeostasis, ATP and reactive oxygen species production, to the needs. These mitochondrial functions are substantially regulated by the post-translational modifications of the mitochondrial proteins among which lysine acetylation is essential. This mitoacetylome is then globally controlled by the balance between spontaneous/enzymatically-catalysed protein acetylation and the NAD+-dependent deacetylation mediated by Sirtuin 3. This enzyme is now considered as a major regulator of the function of the organelle. Regarding the requirement of these mitochondrial adaptations, the subsequent growing interest for this enzyme recently extended to the investigation of the mechanisms driving cell differentiation. This review summarizes the currently available information about the significance of SIRT3 in cell differentiation in physio-pathological contexts. We also suggest a control of the differentiation-activated autophagy by SIRT3, a hypothesis supported by recent findings establishing a causal link between SIRT3 and autophagy. Eventually, an update on the present pharmacological modulators of SIRT3 in a context of cell differentiation is discussed.
Collapse
Affiliation(s)
- Julie Storder
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Thierry Arnould
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium.
| |
Collapse
|
25
|
Nandi SK, Nahomi RB, Harris PS, Michel CR, Fritz KS, Nagaraj RH. The absence of SIRT3 and SIRT5 promotes the acetylation of lens proteins and improves the chaperone activity of α-crystallin in mouse lenses. Exp Eye Res 2019; 182:1-9. [PMID: 30849386 DOI: 10.1016/j.exer.2019.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/13/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
Acetylation of lysine residues occurs in lens proteins. Previous studies have shown an improvement in the chaperone activity of αA-crystallin upon acetylation. Sirtuins are NAD+-dependent enzymes that can deacylate proteins. The roles of sirtuins in regulating the acetylation of lens proteins and their impacts on the function of α-crystallin are not known. Here, we detected sirtuin activity in mouse lenses, and SIRT3 and SIRT5 were present primarily in the mitochondria of cultured primary mouse lens epithelial cells. Western blotting showed higher levels of protein acetylation in the lenses of SIRT3 KO and SIRT5 KO mice than in lenses of WT mice. Mass spectrometry analyses revealed a greater number of acetylated lysine residues in α-crystallin isolated from the SIRT3 and SIRT5 KO lenses than from WT lenses. α-Crystallin isolated from SIRT3 and SIRT5 KO lenses displayed a higher surface hydrophobicity and higher chaperone activity than the protein isolated from WT lenses. Thus, SIRTs regulate the acetylation levels of crystallins in mouse lenses, and acetylation in lenses enhances the chaperone activity of α-crystallin.
Collapse
Affiliation(s)
- Sandip K Nandi
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Rooban B Nahomi
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Peter S Harris
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Cole R Michel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kristofer S Fritz
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ram H Nagaraj
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA; Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA.
| |
Collapse
|
26
|
Shen F, Boccuto L, Pauly R, Srikanth S, Chandrasekaran S. Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome Biol 2019; 20:49. [PMID: 30823893 PMCID: PMC6397465 DOI: 10.1186/s13059-019-1661-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/21/2019] [Indexed: 12/15/2022] Open
Abstract
Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological conditions is a significant challenge. Here, we present a genome-scale network model that predicts the impact of nutritional environment and genetic alterations on histone acetylation. It identifies cell types that are sensitive to histone deacetylase inhibitors based on their metabolic state, and we validate metabolites that alter drug sensitivity. Our model provides a mechanistic framework for predicting how metabolic perturbations contribute to epigenetic changes and sensitivity to deacetylase inhibitors.
Collapse
Affiliation(s)
- Fangzhou Shen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Luigi Boccuto
- Greenwood Genetics Center, Greenwood, SC, 29646, USA
| | - Rini Pauly
- Greenwood Genetics Center, Greenwood, SC, 29646, USA
| | | | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
27
|
Li Y, Chen F, Wei A, Bi F, Zhu X, Yin S, Lin W, Cao W. Klotho recovery by genistein via promoter histone acetylation and DNA demethylation mitigates renal fibrosis in mice. J Mol Med (Berl) 2019; 97:541-52. [PMID: 30806715 DOI: 10.1007/s00109-019-01759-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/16/2018] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
Abstract
Renal fibrosis is a common histomorphological feature of renal aging and chronic kidney diseases of all etiologies, and its initiation and progression are substantially influenced by aberrant epigenetic modifications of fibrosis-susceptible genes, yet without effective therapy. "Epigenetic diets" exhibit tissue-protective and epigenetic-modulating properties; however, their anti-renal fibrosis functions and the underlying mechanisms are less understood. In this study, we show that genistein, a phytoestrogenic isoflavone enriched in dietary soy products, exhibits impressive anti-renal fibrosis activities by recovering epigenetic loss of Klotho, a kidney-enriched anti-aging and fibrosis-suppressing protein. Mouse fibrotic kidneys induced by UUO (unilateral ureteral occlusion) displayed severer Klotho suppression and adverse expression of renal fibrosis-associated proteins, but genistein administration markedly recovered the Klotho loss and attenuated renal fibrosis and the protein expression abnormalities. The examination of possible causes of the Klotho recovery revealed that genistein simultaneously inhibited histone 3 deacetylation of Klotho promoter and normalized the promoter DNA hypermethylation by suppressing elevated DNA methyltransferase DNMT1 and DNMT3a. More importantly, genistein's anti-renal fibrosis effects on the renal fibrotic lesions and the abnormal expressions of fibrosis-associated proteins were abrogated when Klotho is knockdown by RNA interferences in UUO mice. Thus, our results identify Klotho restoration via epigenetic histone acetylation and DNA demethylation as a critical mechanism of genistein's anti-fibrosis function and shed new lights on the potentials of epigenetic diets in preventing or treating aging or renal fibrosis-associated kidney diseases. KEY MESSAGES: Genistein prevents renal fibrosis and the associated Klotho suppression in UUO mice. Genistein upregulates Klotho in part by reversing the promoter histone 3 hypoacetylation. Genistein also preserves Klotho via relieving Klotho promoter hypermethylation. Genistein demethylates Klotho promoter by inhibiting aberrant DNMT1/3a expression. Genistein restoration of Klotho is essential for its anti-renal fibrosis function.
Collapse
|
28
|
Abstract
Lysine acetylation is an important posttranslational modification (PTM) that regulates the function of proteins by affecting their localization, stability, binding, and enzymatic activity. Aberrant acetylation patterns have been observed in numerous diseases, most notably cancer, which has spurred the development of potential therapeutics that target acetylation pathways. Mass spectrometry (MS) has become the most adopted tool not only for the qualitative identification of acetylation sites but also for their large-scale quantification. By using heavy isotope labeling in cell culture combined with MS, it is now possible to accurately quantify newly synthesized acetyl groups and other PTMs, allowing differentiation between dynamically regulated and steady-state modifications. Here, we describe MS-based protocols to identify acetylation sites and quantify acetylation rates on both proteins in general and in the special case of histones. In the experimental approach for the former, 13C-glucose and D3-acetate are used to metabolically label protein acetylation in cells with stable isotopes, thus allowing isotope incorporation to be tracked over time. After protein extraction and digestion, acetylated peptides are enriched via immunoprecipitation and then analyzed by MS. For histones, a similar metabolic labeling approach is performed, followed by acid extraction, derivatization with propionic anhydride, and trypsin digestion prior to MS analysis. The procedures presented may be adapted to investigate acetylation dynamics in a broad range of experimental contexts, including different cell types and stimulation conditions.
Collapse
Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Yekaterina Kori
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
29
|
Lindahl AJ, Lawton AJ, Baeza J, Dowell JA, Denu JM. Site-Specific Lysine Acetylation Stoichiometry Across Subcellular Compartments. Methods Mol Biol 2019; 1983:79-106. [PMID: 31087294 DOI: 10.1007/978-1-4939-9434-2_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Posttranslational modifications of proteins control many complex biological processes, including genome expression, chromatin dynamics, metabolism, and cell division through a language of chemical modifications. Improvements in mass spectrometry-based proteomics have demonstrated protein acetylation is a widespread and dynamic modification in the cell; however, many questions remain on the regulation and downstream effects, and an assessment of the overall acetylation stoichiometry is needed. In this chapter, we describe the determination of acetylation stoichiometry using data-independent acquisition mass spectrometry to expand the number of acetylation sites quantified. However, the increased depth of data-independent acquisition is limited by the spectral library used to deconvolute fragmentation spectra. We describe a powerful approach of subcellular fractionation in conjunction with offline prefractionation to increase the depth of the spectral library. This deep interrogation of subcellular compartments provides essential insights into the compartment-specific regulation and downstream functions of protein acetylation.
Collapse
|
30
|
Novak K, Flöckner L, Erian AM, Freitag P, Herwig C, Pflügl S. Characterizing the effect of expression of an acetyl-CoA synthetase insensitive to acetylation on co-utilization of glucose and acetate in batch and continuous cultures of E. coli W. Microb Cell Fact 2018; 17:109. [PMID: 29986728 PMCID: PMC6036698 DOI: 10.1186/s12934-018-0955-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/17/2018] [Accepted: 07/02/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Due to its high stress tolerance and low acetate secretion, Escherichia coli W is reported to be a good production host for several metabolites and recombinant proteins. However, simultaneous co-utilization of glucose and other substrates such as acetate remains a challenge. The activity of acetyl-CoA-synthetase, one of the key enzymes involved in acetate assimilation is tightly regulated on a transcriptional and post-translational level. The aim of this study was to engineer E. coli W for overexpression of an acetylation insensitive acetyl-CoA-synthetase and to characterize this strain in batch and continuous cultures using glucose, acetate and during co-utilization of both substrates. RESULTS Escherichia coli W engineered to overexpress an acetylation-insensitive acetyl-CoA synthetase showed a 2.7-fold increase in acetate uptake in a batch process containing glucose and high concentrations of acetate compared to a control strain, indicating more efficient co-consumption of glucose and acetate. When acetate was used as the carbon source, batch duration could significantly be decreased in the overexpression strain, possibly due to alleviation of acetate toxicity. Chemostat cultivations with different dilution rates using glucose revealed only minor differences between the overexpression and control strain. Accelerostat cultivations using dilution rates between 0.20 and 0.70 h-1 indicated that E. coli W is naturally capable of efficiently co-utilizing glucose and acetate over a broad range of specific growth rates. Expression of acetyl-CoA synthetase resulted in acetate and glucose accumulation at lower dilution rates compared to the control strain. This observation can possibly be attributed to a higher ratio between acs and pta-ackA in the overexpression strain as revealed by gene expression analysis. This would result in enhanced energy dissipation caused by an imbalance in the Pta-AckA-Acs cycle. Furthermore, yjcH and actP, genes co-transcribed with acetyl-CoA synthetase showed significant down-regulation at elevated dilution rates. CONCLUSIONS Escherichia coli W expressing an acetylation-insensitive acetyl-CoA synthetase was shown to be a promising candidate for mixed feed processes using glucose and acetate. Comparison between batch and continuous cultures revealed distinct differences in glucose-acetate co-utilization behavior, requiring additional investigations such as multi-omics analysis and further engineering towards even more efficient co-utilization strains of E. coli W.
Collapse
Affiliation(s)
- Katharina Novak
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Lukas Flöckner
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Anna Maria Erian
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Philipp Freitag
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christoph Herwig
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Research Area Biochemical Engineering, Institute for Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| |
Collapse
|
31
|
Abstract
Posttranslational modification (PTM) of proteins has emerged as a major regulatory mechanism in all three domains of life. One emerging PTM is Nε-lysine acetylation-the acetylation of the epsilon amino group of lysine residues. Nε-lysine acetylation is known to regulate multiple cellular processes. In eukaryotes, it regulates chromatin structure, transcription, metabolism, signal transduction, and the cytoskeleton. Recently, multiple groups have detected Nε-lysine acetylation in diverse bacterial phyla, but no work on protein acetylation in Borrelia burgdorferi has been reported. Here, we describe a step-by-step protocol to identify Nε-lysine acetylated proteins in B. burgdorferi.
Collapse
|
32
|
Dutto I, Scalera C, Prosperi E. CREBBP and p300 lysine acetyl transferases in the DNA damage response. Cell Mol Life Sci 2018; 75:1325-1338. [PMID: 29170789 DOI: 10.1007/s00018-017-2717-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/21/2022]
Abstract
The CREB-binding protein (CREBBP, or in short CBP) and p300 are lysine (K) acetyl transferases (KAT) belonging to the KAT3 family of proteins known to modify histones, as well as non-histone proteins, thereby regulating chromatin accessibility and transcription. Previous studies have indicated a tumor suppressor function for these enzymes. Recently, they have been found to acetylate key factors involved in DNA replication, and in different DNA repair processes, such as base excision repair, nucleotide excision repair, and non-homologous end joining. The growing list of CBP/p300 substrates now includes factors involved in DNA damage signaling, and in other pathways of the DNA damage response (DDR). This review will focus on the role of CBP and p300 in the acetylation of DDR proteins, and will discuss how this post-translational modification influences their functions at different levels, including catalytic activity, DNA binding, nuclear localization, and protein turnover. In addition, we will exemplify how these functions may be necessary to efficiently coordinate the spatio-temporal response to DNA damage. CBP and p300 may contribute to genome stability by fine-tuning the functions of DNA damage signaling and DNA repair factors, thereby expanding their role as tumor suppressors.
Collapse
Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
- IRB, Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Claudia Scalera
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| |
Collapse
|
33
|
Lafarga V, Tapia O, Sharma S, Bengoechea R, Stoecklin G, Lafarga M, Berciano MT. CBP-mediated SMN acetylation modulates Cajal body biogenesis and the cytoplasmic targeting of SMN. Cell Mol Life Sci 2018; 75:527-46. [PMID: 28879433 DOI: 10.1007/s00018-017-2638-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 08/29/2017] [Indexed: 01/12/2023]
Abstract
The survival of motor neuron (SMN) protein plays an essential role in the biogenesis of spliceosomal snRNPs and the molecular assembly of Cajal bodies (CBs). Deletion of or mutations in the SMN1 gene cause spinal muscular atrophy (SMA) with degeneration and loss of motor neurons. Reduced SMN levels in SMA lead to deficient snRNP biogenesis with consequent splicing pathology. Here, we demonstrate that SMN is a novel and specific target of the acetyltransferase CBP (CREB-binding protein). Furthermore, we identify lysine (K) 119 as the main acetylation site in SMN. Importantly, SMN acetylation enhances its cytoplasmic localization, causes depletion of CBs, and reduces the accumulation of snRNPs in nuclear speckles. In contrast, the acetylation-deficient SMNK119R mutant promotes formation of CBs and a novel category of promyelocytic leukemia (PML) bodies enriched in this protein. Acetylation increases the half-life of SMN protein, reduces its cytoplasmic diffusion rate and modifies its interactome. Hence, SMN acetylation leads to its dysfunction, which explains the ineffectiveness of HDAC (histone deacetylases) inhibitors in SMA therapy despite their potential to increase SMN levels.
Collapse
|
34
|
Zhang L, Chen CL, Kang PT, Jin Z, Chen YR. Differential protein acetylation assists import of excess SOD2 into mitochondria and mediates SOD2 aggregation associated with cardiac hypertrophy in the murine SOD2-tg heart. Free Radic Biol Med 2017; 108:595-609. [PMID: 28433661 PMCID: PMC5487267 DOI: 10.1016/j.freeradbiomed.2017.04.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 12/28/2022]
Abstract
SOD2 is the primary antioxidant enzyme neutralizing •O2- in mitochondria. Cardiac-specific SOD2 overexpression (SOD2-tg) induces supernormal function and cardiac hypertrophy in the mouse heart. However, the reductive stress imposed by SOD2 overexpression results in protein aggregation of SOD2 pentamers and differential hyperacetylation of SOD2 in the mitochondria and cytosol. Here, we studied SOD2 acetylation in SOD2-tg and wild-type mouse hearts. LC-MS/MS analysis indicated the presence of four acetylated lysines in matrix SOD2 and nine acetylated lysines in cytosolic SOD2 from the SOD2-tg heart. However, only one specific acetylated lysine residue was detected in the mitochondria of the wild-type heart, which was consistent with Sirt3 downregulation in the SOD2-tg heart. LC-MS/MS further detected hyperacetylated SOD2 with a signaling peptide in the mitochondrial inner membrane and matrix of the SOD2-tg heart, indicating partial arrest of the SOD2 precursor in the membrane during translocation into the mitochondria. Upregulation of HSP 70 and cytosolic HSP 60 enabled the translocation of excess SOD2 into mitochondria. In vitro acetylation of matrix SOD2 with Ac2O deaggregated pentameric SOD2, restored the profile of cytosolic SOD2 hyperacetylation, and decreased matrix SOD2 activity. As revealed by 3D structure, acetylation of K89, K134, and K154 of cytosolic SOD2 induces unfolding of the tertiary structure and breaking of the salt bridges that are important for the quaternary structure, suggesting that hyperacetylation and HSP 70 upregulation maintain the unfolded status of SOD2 in the cytosol and mediate the import of SOD2 across the membrane. Downregulation of Sirt3, HSP 60, and presequence protease in the mitochondria of the SOD2-tg heart promoted protein misfolding that led to pentameric aggregation.
Collapse
Affiliation(s)
- Liwen Zhang
- Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Chwen-Lih Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Patrick T Kang
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Zhicheng Jin
- Department of Pharmaceutical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Yeong-Renn Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
| |
Collapse
|
35
|
Abstract
Determining protein acetylation by immunoprecipitation and immunoblotting can be challenging, especially if the tissue of interest is low in quantity, and when good quality acetylation site-specific antibodies are not available. Proximity ligation assays allow a sensitive and quantitative method to assess Foxp3 acetylation in regulatory T cells, with as little as 1.5 × 105 cells within two days turnaround time. This method is of potential use in other similar scenarios, when post-translational modifications of a protein of interest need to be determined with only a small amount of sample and in the absence of specific antibodies that can assess the post-translational modification in the protein of interest.
Collapse
Affiliation(s)
- Jing Jiao
- Division of Nephrology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Boulevard, 916C Abramson Research Center, Philadelphia, PA, 19104-4318, USA
| | - Rongxiang Han
- Laboratory Medicine and Biesecker Center for Pediatric Liver Disease, Division of Transplant Immunology, Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Wayne W Hancock
- Laboratory Medicine and Biesecker Center for Pediatric Liver Disease, Division of Transplant Immunology, Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ulf H Beier
- Division of Nephrology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Boulevard, 916C Abramson Research Center, Philadelphia, PA, 19104-4318, USA.
| |
Collapse
|
36
|
Fukada M, Nakayama A, Mamiya T, Yao TP, Kawaguchi Y. Dopaminergic abnormalities in Hdac6-deficient mice. Neuropharmacology 2016; 110:470-479. [PMID: 27544826 DOI: 10.1016/j.neuropharm.2016.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/15/2016] [Accepted: 08/15/2016] [Indexed: 11/26/2022]
Abstract
Histone deacetylase 6 (Hdac6), a multifunctional cytoplasmic deacetylase, is abundant in brain. We previously demonstrated that global Hdac6 depletion causes aberrant emotional behaviors in mice. Identification of affected brain systems and its molecular basis will lead to new insights into relations between protein acetylation events and psychiatric disorders. Here we report the dopaminergic abnormalities in Hdac6 KO mice. The dopamine transmission mediated by D1-like and D2-like G protein-coupled dopamine receptors is known to play roles in controlling movement, cognition, and motivational processes, and its dysfunction causes psychiatric disorders. We found that Hdac6 KO mice showed significantly increased locomotor response to novel, but not to habituated environment. In addition, Hdac6 KO mice showed a long-lasting sensitivity to psychostimulants, increased locomotor response to D2-like, but not D1 dopamine receptor agonists, and rapid locomotor response to apomorphine, a direct dopamine agonist, in dopamine-depleted condition. Hdac6 protein was expressed in dopaminergic neurons and their terminals in adult mice brain, and Hdac6-depletion augmented acetylation levels of dopamine-enriched synaptosomal proteins. In Hdac6 KO mice, the striatal content of dopamine and its metabolites was normal in basal condition, but mRNA level of D2 dopamine receptor in the striatum was decreased by 30%. Taken together, our results provide evidence that Hdac6 deficiency leads to aberrant dopamine-dependent behaviors by enhancing postsynaptic dopamine D2 receptor response. This study points out the possibility that Hdac6 and reversible-acetylation events play a regulatory role in D2 dopamine receptor signaling, and thus participate in the pathology of the dopamine-related psychiatric disorders such as schizophrenia.
Collapse
Affiliation(s)
- Masahide Fukada
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - Atsuo Nakayama
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - Takayoshi Mamiya
- Department of Chemical Pharmacology, Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan
| | - Tso-Pang Yao
- Department of Pharmacology and Cancer Biology, Duke University, North Carolina, USA
| | - Yoshiharu Kawaguchi
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan.
| |
Collapse
|
37
|
Fan J, Alsarraf O, Chou CJ, Yates PW, Goodwin NC, Rice DS, Crosson CE. Ischemic preconditioning, retinal neuroprotection and histone deacetylase activities. Exp Eye Res 2016; 146:269-275. [PMID: 27060376 DOI: 10.1016/j.exer.2016.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/07/2016] [Accepted: 03/31/2016] [Indexed: 01/05/2023]
Abstract
Increased histone deacetylase (HDAC) activity and the resulting dysregulation of protein acetylation is an integral event in retinal degenerations associated with ischemia and ocular hypertension. This study investigates the role of preconditioning on the process of acetylation in ischemic retinal injury. Rat eyes were unilaterally subjected to retinal injury by 45 min of acute ischemia, and retinal neuroprotection induced by 5 min of an ischemic preconditioning (IPC) event. HDAC activity was evaluated by a fluorometric enzymatic assay with selective isoform inhibitors. Retinal localization of acetylated histone-H3 was determined by immunohistochemistry on retina cross sections. Cleaved caspase-3 level was evaluated by Western blots. Electroretinogram (ERG) analyses were used to assess differences in retinal function seven days following ischemic injury. In control eyes, analysis of HDAC isoforms demonstrated that HDAC1/2 accounted for 28.4 ± 1.6%, HDAC3 for 42.4 ± 1.5% and HDAC6 activity 27.3 ± 3.5% of total activity. Following ischemia, total Class-I HDAC activity increased by 21.2 ± 6.2%, and this increase resulted solely from a rise in HDAC1/2 activity. No change in HDAC3 activity was measured. Activity of Class-II HDACs and HDAC8 was negligible. IPC stimulus prior to ischemic injury also suppressed the rise in Class-I HDAC activity, cleaved caspase-3 levels, and increased acetylated histone-H3 in the retina. In control animals 7 days post ischemia, ERG a- and b-wave amplitudes were significantly reduced by 34.9 ± 3.1% and 42.4 ± 6.3%, respectively. In rats receiving an IPC stimulus, the ischemia-induced decline in ERG a- and b-wave amplitudes was blocked. Although multiple HDACs were detected in the retina, these studies provide evidence that hypoacetylation associated with ischemic injury results from the selective rise in HDAC1/2 activity and that neuroprotection induced by IPC is mediated in part by suppressing HDAC activity.
Collapse
Affiliation(s)
- Jie Fan
- 167 Ashley Avenue, Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Oday Alsarraf
- 167 Ashley Avenue, Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - C James Chou
- 167 Ashley Avenue, Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Phillip W Yates
- 167 Ashley Avenue, Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Dennis S Rice
- Lexicon Pharmaceuticals, The Woodlands, TX, 77381, USA
| | - Craig E Crosson
- 167 Ashley Avenue, Storm Eye Institute, Department of Ophthalmology, Medical University of South Carolina, Charleston, SC, 29425, USA
| |
Collapse
|
38
|
Wollebo HS, Bellizzi A, Cossari DH, Salkind J, Safak M, White MK. The Brd4 acetyllysine-binding protein is involved in activation of polyomavirus JC. J Neurovirol 2016; 22:615-625. [PMID: 27007123 DOI: 10.1007/s13365-016-0435-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/26/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Brd4 is an epigenetic reader protein and a member of the BET (bromodomain and extra terminal domain) family of proteins with two bromodomains that recognize acetylated lysine residues. Brd4 specifically binds to acetylated transcription factor NF-κB p65 and coactivates transcription. Polyomavirus JC (JCV) is regulated by a noncoding control region (NCCR) containing promoter/enhancer elements for viral gene expression including a binding site for NF-κB, which responds to proinflammatory cytokines such as TNF-α, the DNA damage response, calcium signaling and acetylation of the NF-κB p65 subunit on lysine residues K218 and K221. Earlier studies indicated that NF-κB is involved in the reactivation of persistent/latent JCV in glial cells to cause progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease of the brain caused by replication of JCV in glial cells. To investigate the mechanism of action of NF-κB acetylation on JCV transcription, we examined Brd4 and found that JCV early transcription was stimulated by Brd4 via the JCV NF-κB site and that p65 K218 and K221 were involved. Treatment with the Brd4 inhibitor JQ1(+) or mutation of either K218 or K221 to glutamine (K218R or K221) inhibited this stimulation and decreased the proportion of p65 in the nucleus. We conclude that Brd4 is involved in the regulation of the activation status of JCV in glial cells.
Collapse
Affiliation(s)
- Hassen S Wollebo
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Anna Bellizzi
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Dominique H Cossari
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Julian Salkind
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Mahmut Safak
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Martyn K White
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
| |
Collapse
|
39
|
Esipov RS, Makarov DA, Stepanenko VN, Miroshnikov AI. Development of the intein-mediated method for production of recombinant thymosin β4 from the acetylated in vivo fusion protein. J Biotechnol 2016; 228:73-81. [PMID: 27015974 DOI: 10.1016/j.jbiotec.2016.02.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
Thymosin β4 is a 43 amino acid long peptide with an acetylated N-terminal serin that has a high potential as a remedy for healing ulcers, wounds and burns. Although protein biosynthesis offers attractive opportunities in terms of a large-scale production, currently thymosin β4 is mainly produced by chemical synthesis. The problems that hinder the successful commercialization of the biotechnological approach are associated with the small peptides expression and N-terminal acetylation. This work presents an innovative biotechnological method for thymosin β4 production that employs the peptide acetylation in vivo. A genetically engineered construct was created, where the Tβ4 coding sequence fused with the intein Mxe GyrA sequence and chitin-binding domain was combined with the acetyltransferase coding sequence to form a polycistronic construct under a stringent control of T7 promoter. This plasmid construct provided for the expression of the Tβ4-intein fusion protein. In the process of the post-translational modification in vivo formyl methionine was completely removed from the target peptide N-terminus and followed by the Tβ4 precursor N-terminal acetylation. The use of the intein-mediated expression system made it possible to extract thymosin β4 in only 2 chromatographic runs. The method is straightforward to implement and scale up.
Collapse
Affiliation(s)
- Roman S Esipov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russian Federation.
| | - Dmitry A Makarov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russian Federation.
| | - Vasily N Stepanenko
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russian Federation.
| | - Anatoly I Miroshnikov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russian Federation.
| |
Collapse
|
40
|
Li Z, Li X, Wang Z, Shen QW, Zhang D. Antemortem stress regulates protein acetylation and glycolysis in postmortem muscle. Food Chem 2016; 202:94-8. [PMID: 26920270 DOI: 10.1016/j.foodchem.2016.01.085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 12/24/2015] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
Abstract
Although exhaustive research has established that preslaughter stress is a major factor contributing to pale, soft, exudative (PSE) meat, questions remain regarding the biochemistry of postmortem glycolysis. In this study, the influence of preslaughter stress on protein acetylation in relationship to glycolysis was studied. The data show that antemortem swimming significantly enhanced glycolysis and the total acetylated proteins in postmortem longissimus dorsi (LD) muscle of mice. Inhibition of protein acetylation by histone acetyltransferase (HAT) inhibitors eliminated stress induced increase in glycolysis. Inversely, antemortem injection of histone deacetylase (HDAC) inhibitors, trichostatin A (TSA) and nicotinamide (NAM), further increased protein acetylation early postmortem and the glycolysis. These data provide new insight into the biochemistry of postmortem glycolysis by showing that protein acetylation regulates glycolysis, which may participate in the regulation of preslaughter stress on glycolysis in postmortem muscle.
Collapse
Affiliation(s)
- Zhongwen Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, PR China; College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, PR China
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, PR China
| | - Qingwu W Shen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, PR China; College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China.
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, PR China.
| |
Collapse
|
41
|
Storey KB. Comparative enzymology-new insights from studies of an "old" enzyme, lactate dehydrogenase. Comp Biochem Physiol B Biochem Mol Biol 2015; 199:13-20. [PMID: 26688543 DOI: 10.1016/j.cbpb.2015.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/12/2022]
Abstract
Comparative enzymology explores the molecular mechanisms that alter the properties of enzymes to best fit and adapt them to the biotic demands and abiotic stresses that affect the cellular environment in which these protein catalysts function. For many years, comparative enzymology was primarily concerned with analyzing enzyme functional properties (e.g. substrate affinities, allosteric effectors, responses to temperature or pH, stabilizers, denaturants, etc.) in order to determine how enzyme properties were optimized to function under changing conditions. More recently it became apparent that posttranslational modifications of enzymes play a huge role in metabolic regulation. At first, such modifications appeared to target just crucial regulatory enzymes but recent work is showing that many dehydrogenases are also targets of posttranslational modification leading to substantial changes in enzyme properties. The present article focuses in particular on lactate dehydrogenase (LDH) showing that stress-induced changes in enzyme properties can be linked with reversible posttranslational modifications; e.g. changes in the phosphorylation state of LDH occur in response to dehydration stress in frogs and anoxia exposure of turtles and snails. Furthermore, these studies show that LDH is also a target of other posttranslational modifications including acetylation, methylation and ubiquitination that change in response to anoxia or dehydration stress. Selected new methods for exploring posttranslational modifications of dehydrogenases are discussed and new challenges for the future of comparative enzymology are presented that will help to achieve a deeper understanding of biochemical adaptation through enzyme regulation.
Collapse
Affiliation(s)
- Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
| |
Collapse
|
42
|
Kerner J, Yohannes E, Lee K, Virmani A, Koverech A, Cavazza C, Chance MR, Hoppel C. Acetyl-L-carnitine increases mitochondrial protein acetylation in the aged rat heart. Mech Ageing Dev 2015; 145:39-50. [PMID: 25660059 DOI: 10.1016/j.mad.2015.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/24/2014] [Accepted: 01/27/2015] [Indexed: 12/30/2022]
Abstract
Previously we showed that in vivo treatment of elderly Fisher 344 rats with acetylcarnitine abolished the age-associated defect in respiratory chain complex III in interfibrillar mitochondria and improved the functional recovery of the ischemic/reperfused heart. Herein, we explored mitochondrial protein acetylation as a possible mechanism for acetylcarnitine's effect. In vivo treatment of elderly rats with acetylcarnitine restored cardiac acetylcarnitine content and increased mitochondrial protein lysine acetylation and increased the number of lysine-acetylated proteins in cardiac subsarcolemmal and interfibrillar mitochondria. Enzymes of the tricarboxylic acid cycle, mitochondrial β-oxidation, and ATP synthase of the respiratory chain showed the greatest acetylation. Acetylation of isocitrate dehydrogenase, long-chain acyl-CoA dehydrogenase, complex V, and aspartate aminotransferase was accompanied by decreased catalytic activity. Several proteins were found to be acetylated only after treatment with acetylcarnitine, suggesting that exogenous acetylcarnitine served as the acetyl-donor. Two-dimensional fluorescence difference gel electrophoresis analysis revealed that acetylcarnitine treatment also induced changes in mitochondrial protein amount; a two-fold or greater increase/decrease in abundance was observed for thirty one proteins. Collectively, our data provide evidence for the first time that in the aged rat heart in vivo administration of acetylcarnitine provides acetyl groups for protein acetylation and affects the amount of mitochondrial proteins.
Collapse
|
43
|
Ma C, Pathak C, Jang S, Lee SJ, Nam M, Kim SJ, Im H, Lee BJ. Structure of Thermoplasma volcanium Ard1 belongs to N-acetyltransferase family member suggesting multiple ligand binding modes with acetyl coenzyme A and coenzyme A. Biochim Biophys Acta 2014; 1844:1790-7. [PMID: 25062911 DOI: 10.1016/j.bbapap.2014.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
Abstract
Acetylation and deacetylation reactions result in biologically important modifications that are involved in normal cell function and cancer development. These reactions, carried out by protein acetyltransferase enzymes, act by transferring an acetyl group from acetyl-coenzymeA (Ac-CoA) to various substrate proteins. Such protein acetylation remains poorly understood in Archaea, and has been only partially described. Information processing in Archaea has been reported to be similar to that in eukaryotes and distinct from the equivalent bacterial processes. The human N-acetyltransferase Ard1 (hArd1) is one of the acetyltransferases that has been found to be overexpressed in various cancer cells and tissues, and knockout of the hArd1 gene significantly reduces growth rate of the cancer cell lines. In the present study, we determined the crystal structure of Thermoplasma volcanium Ard1 (Tv Ard1), which shows both ligand-free and multiple ligand-bound forms, i.e.,Ac-CoA- and coenzyme A (CoA)-bound forms. The difference between ligand-free and ligand-bound chains in the crystal structure was used to search for the interacting residues. The re-orientation and position of the loop between β4 and α3 including the phosphate-binding loop (P-loop) were observed, which are important for the ligand interaction. In addition, a biochemical assay to determine the N-acetyltransferase activity of Tv Ard1 was performed using the T.volcanium substrate protein Alba (Tv Alba). Taken together, the findings of this study elucidate ligand-free form of Tv Ard1 for the first time and suggest multiple modes of binding with Ac-CoA and CoA.
Collapse
Affiliation(s)
- Chao Ma
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Chinar Pathak
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sunbok Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Sang Jae Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Minjoo Nam
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea.
| |
Collapse
|
44
|
Wirth M, Karaca S, Wenzel D, Ho L, Tishkoff D, Lombard DB, Verdin E, Urlaub H, Jedrusik-Bode M, Fischle W. Mitochondrial SIRT4-type proteins in Caenorhabditis elegans and mammals interact with pyruvate carboxylase and other acetylated biotin-dependent carboxylases. Mitochondrion 2013; 13:705-20. [PMID: 23438705 DOI: 10.1016/j.mito.2013.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 02/03/2013] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
Abstract
The biological and enzymatic function of SIRT4 is largely uncharacterized. We show that the Caenorhabditis elegans SIR-2.2 and SIR-2.3 orthologs of SIRT4 are ubiquitously expressed, also localize to mitochondria and function during oxidative stress. Further, we identified conserved interaction with mitochondrial biotin-dependent carboxylases (PC, PCC, MCCC), key enzymes in anaplerosis and ketone body formation. The carboxylases were found acetylated on multiple lysine residues and detailed analysis of mPC suggested that one of these residues, K748ac, might regulate enzymatic activity. Nevertheless, no changes in mPC acetylation levels and enzymatic activity could be detected upon overexpression or loss of functional SIRT4.
Collapse
|