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Huang Q, Yao Y, Wang Y, Li J, Chen J, Wu M, Guo C, Lou J, Yang W, Zhao L, Tong X, Zhao D, Li X. Ginsenoside Rb2 inhibits p300-mediated SF3A2 acetylation at lysine 10 to promote Fscn1 alternative splicing against myocardial ischemic/reperfusion injury. J Adv Res 2024; 65:365-379. [PMID: 38101749 DOI: 10.1016/j.jare.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
INTRODUCTION Ginsenosides (GS) derived from Panax ginseng can regulate protein acetylation to promote mitochondrial function for protecting cardiomyocytes. However, the potential mechanisms of GS for regulating acetylation modification are not yet clear. OBJECTIVES This study aimed to explore the potential mechanisms of GS in regulating protein acetylation and identify ginsenoside monomer for fighting myocardial ischemia-related diseases. METHODS The 4D-lable free acetylomic analysis was employed to gain the acetylated proteins regulated by GS pretreatment. The co-immunoprecipitation assay, immunofluorescent staining, and mitochondrial respiration measurement were performed to detect the effect of GS or ginsenoside monomer on acetylated protein level and mitochondrial function. RNA sequencing, site-specific mutation, and shRNA interference were used to explore the downstream targets of acetylation modificationby GS. Cellular thermal shift assay and surface plasmon resonance were used for identifying the binding of ginsenoside with target protein. RESULTS In the cardiomyocytes of normal, oxygen glucose deprivation and/or reperfusion conditions, the acetylomic analysis identified that the acetylated levels of spliceosome proteins were inhibited by GS pretreatment and SF3A2 acetylation at lysine 10 (K10) was significantly decreased as a potential target of GS. Ginsenoside Rb2 was identified as one of the active ginsenoside monomers for reducing the acetylation of SF3A2 (K10), which enhanced mitochondrial respiration against myocardial ischemic injury in in vivo and in vitro experiments. RNA-seq analysis showed that ginsenoside Rb2 promoted alternative splicing of mitochondrial function-related genes and the level of fascin actin-bundling protein 1 (Fscn1) was obviously upregulated, which was dependent on SF3A2 acetylation. Critically, thermodynamic, kinetic and enzymatic experiments demonstrated that ginsenoside Rb2 directly interacted with p300 for inhibiting its activity. CONCLUSION These findings provide a novel mechanism underlying cardiomyocyte protection of ginsenoside Rb2 by inhibiting p300-mediated SF3A2 acteylation for promoting Fscn1 expression, which might be a promising approach for the prevention and treatment of myocardial ischemic diseases.
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Affiliation(s)
- Qingxia Huang
- Research Center of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130021, China; Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Yao Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Yisa Wang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Jing Li
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Jinjin Chen
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Mingxia Wu
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Chen Guo
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Jia Lou
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin 301617, China
| | - Wenzhi Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin 301617, China
| | - Linhua Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
| | - Xiaolin Tong
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China.
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China.
| | - Xiangyan Li
- Northeast Asia Research Institute of Traditional Chinese Medicine, Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Jilin Provincial Key Laboratory of Bio-Macromolecules of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin 130117, China.
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Huang Z, Zeng L, Cheng B, Li D. Overview of class I HDAC modulators: Inhibitors and degraders. Eur J Med Chem 2024; 276:116696. [PMID: 39094429 DOI: 10.1016/j.ejmech.2024.116696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/28/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
Class I histone deacetylases (HDACs) are closely associated with the development of a diverse array of diseases, including cancer, neurodegenerative disorders, HIV, and inflammatory diseases. Considering the essential roles in tumorigenesis, class I HDACs have emerged as highly desirable targets for therapeutic strategies, particularly in the field of anticancer drug development. However, the conventional class I HDAC inhibitors faced several challenges such as acquired resistance, inherent toxicities, and limited efficacy in inhibiting non-enzymatic functions of HDAC. To address these problems, novel strategies have emerged, including the development of class I HDAC dual-acting inhibitors, targeted protein degradation (TPD) technologies such as PROTACs, molecular glues, and HyT degraders, as well as covalent inhibitors. This review provides a comprehensive overview of class I HDAC enzymes and inhibitors, by initially introducing their structure and biological roles. Subsequently, we focus on the recent advancements of class I HDAC modulators, including isoform-selective class I inhibitors, dual-target inhibitors, TPDs, and covalent inhibitors, from the perspectives of rational design principles, pharmacodynamics, pharmacokinetics, and clinical progress. Finally, we also provide the challenges and outlines future prospects in the realm of class I HDAC-targeted drug discovery for cancer therapeutics.
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Affiliation(s)
- Ziqian Huang
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou, 314000, China
| | - Binbin Cheng
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, China.
| | - Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
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3
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Guo L. F-ATP synthase inhibitory factor 1 and mitochondria-organelle interactions: New insight and implications. Pharmacol Res 2024; 208:107393. [PMID: 39233058 DOI: 10.1016/j.phrs.2024.107393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/08/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Mitochondria are metabolic hub, and act as primary sites for reactive oxygen species (ROS) and metabolites generation. Mitochondrial Ca2+ uptake contributes to Ca2+ storage. Mitochondria-organelle interactions are important for cellular metabolic adaptation, biosynthesis, redox balance, cell fate. Organelle communications are mediated by Ca2+/ROS signals, vesicle transport and membrane contact sites. The permeability transition pore (PTP) is an unselective channel that provides a release pathway for Ca2+/ROS, mtDNA and metabolites. F-ATP synthase inhibitory factor 1 (IF1) participates in regulation of PTP opening and is required for the translocation of transcriptional factors c-Myc/PGC1α to mitochondria to stimulate metabolic switch. IF1, a mitochondrial specific protein, has been suggested to regulate other organelles including nucleus, endoplasmic reticulum and lysosomes. IF1 may be able to mediate mitochondria-organelle interactions and cellular physiology through regulation of PTP activity.
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Affiliation(s)
- Lishu Guo
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China; Department of Anesthesiology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Li H, Liu C, Li R, Zhou L, Ran Y, Yang Q, Huang H, Lu H, Song H, Yang B, Ru H, Lin S, Zhang L. AARS1 and AARS2 sense L-lactate to regulate cGAS as global lysine lactyltransferases. Nature 2024:10.1038/s41586-024-07992-y. [PMID: 39322678 DOI: 10.1038/s41586-024-07992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/27/2024] [Indexed: 09/27/2024]
Abstract
L-lactate modifies proteins through lactylation1, but how this process occurs is unclear. Here we identify the alanyl-tRNA synthetases AARS1 and AARS2 (AARS1/2) as intracellular L-lactate sensors required for L-lactate to stimulate the lysine lactylome in cells. AARS1/2 and the evolutionarily conserved Escherichia coli orthologue AlaRS bind to L-lactate with micromolar affinity and they directly catalyse L-lactate for ATP-dependent lactylation on the lysine acceptor end. In response to L-lactate, AARS2 associates with cyclic GMP-AMP synthase (cGAS) and mediates its lactylation and inactivation in cells and in mice. By establishing a genetic code expansion orthogonal system for lactyl-lysine incorporation, we demonstrate that the presence of a lactyl moiety at a specific cGAS amino-terminal site abolishes cGAS liquid-like phase separation and DNA sensing in vitro and in vivo. A lactyl mimetic knock-in inhibits cGAS, whereas a lactyl-resistant knock-in protects mice against innate immune evasion induced through high levels of L-lactate. MCT1 blockade inhibits cGAS lactylation in stressed mice and restores innate immune surveillance, which in turn antagonizes viral replication. Thus, AARS1/2 are conserved intracellular L-lactate sensors and have an essential role as lactyltransferases. Moreover, a chemical reaction process of lactylation targets and inactivates cGAS.
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Affiliation(s)
- Heyu Li
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Ran Li
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, Hangzhou City University School of Medicine, Hangzhou, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Yu Ran
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiqing Yang
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Huizhe Huang
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huasong Lu
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Hai Song
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Bing Yang
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Heng Ru
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Long Zhang
- Life Sciences Institute and State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of the Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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5
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Chen LY, Singha Roy SJ, Jadhav AM, Wang WW, Chen PH, Bishop T, Erb MA, Parker CG. Functional Investigations of p53 Acetylation Enabled by Heterobifunctional Molecules. ACS Chem Biol 2024; 19:1918-1929. [PMID: 39250704 PMCID: PMC11421428 DOI: 10.1021/acschembio.4c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/11/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate the critical stress response and tumor suppressive functions of p53. Among these, acetylation events mediated by multiple acetyltransferases lead to differential target gene activation and subsequent cell fate. However, our understanding of these events is incomplete due to, in part, the inability to selectively and dynamically control p53 acetylation. We recently developed a heterobifunctional small molecule system, AceTAG, to direct the acetyltransferase p300/CBP for targeted protein acetylation in cells. Here, we expand AceTAG to leverage the acetyltransferase PCAF/GCN5 and apply these tools to investigate the functional consequences of targeted p53 acetylation in human cancer cells. We demonstrate that the recruitment of p300/CBP or PCAF/GCN5 to p53 results in distinct acetylation events and differentiated transcriptional activities. Further, we show that chemically induced acetylation of multiple hotspot p53 mutants results in increased stabilization and enhancement of transcriptional activity. Collectively, these studies demonstrate the utility of AceTAG for functional investigations of protein acetylation.
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Affiliation(s)
- Li-Yun Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Soumya Jyoti Singha Roy
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Appaso M. Jadhav
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Wesley W. Wang
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pei-Hsin Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Timothy Bishop
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael A. Erb
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher G. Parker
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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6
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Zhang Z, Zeng Y, Hou J, Li L. Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation. PLANTA 2024; 260:93. [PMID: 39264431 DOI: 10.1007/s00425-024-04518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
MAIN CONCLUSION This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Zeng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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7
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Li X, Yu T, Li X, He X, Zhang B, Yang Y. Role of novel protein acylation modifications in immunity and its related diseases. Immunology 2024; 173:53-75. [PMID: 38866391 DOI: 10.1111/imm.13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
The cross-regulation of immunity and metabolism is currently a research hotspot in life sciences and immunology. Metabolic immunology plays an important role in cutting-edge fields such as metabolic regulatory mechanisms in immune cell development and function, and metabolic targets and immune-related disease pathways. Protein post-translational modification (PTM) is a key epigenetic mechanism that regulates various biological processes and highlights metabolite functions. Currently, more than 400 PTM types have been identified to affect the functions of several proteins. Among these, metabolic PTMs, particularly various newly identified histone or non-histone acylation modifications, can effectively regulate various functions, processes and diseases of the immune system, as well as immune-related diseases. Thus, drugs aimed at targeted acylation modification can have substantial therapeutic potential in regulating immunity, indicating a new direction for further clinical translational research. This review summarises the characteristics and functions of seven novel lysine acylation modifications, including succinylation, S-palmitoylation, lactylation, crotonylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation and malonylation, and their association with immunity, thereby providing valuable references for the diagnosis and treatment of immune disorders associated with new acylation modifications.
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Affiliation(s)
- Xiaoqian Li
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiaolu Li
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiangqin He
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Bei Zhang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
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Stacpoole PW, Dirain CO. The pyruvate dehydrogenase complex at the epigenetic crossroads of acetylation and lactylation. Mol Genet Metab 2024; 143:108540. [PMID: 39067348 DOI: 10.1016/j.ymgme.2024.108540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
The pyruvate dehydrogenase complex (PDC) is remarkable for its size and structure as well as for its physiological and pathological importance. Its canonical location is in the mitochondrial matrix, where it primes the tricarboxylic acid (TCA) cycle by decarboxylating glycolytically-derived pyruvate to acetyl-CoA. Less well appreciated is its role in helping to shape the epigenetic landscape, from early development throughout mammalian life by its ability to "moonlight" in the nucleus, with major repercussions for human healthspan and lifespan. The PDC's influence on two crucial modifiers of the epigenome, acetylation and lactylation, is the focus of this brief review.
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Affiliation(s)
- Peter W Stacpoole
- University of Florida, College of Medicine Department of Medicine, Department of Biochemistry & Molecular Biology, Gainesville, FL, United States.
| | - Carolyn O Dirain
- University of Florida, College of Medicine Department of Medicine, Gainesville, FL, United States
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Jeon KI, Kumar A, Brookes PS, Nehrke K, Huxlin KR. Manipulating mitochondrial pyruvate carrier function causes metabolic remodeling in corneal myofibroblasts that ameliorates fibrosis. Redox Biol 2024; 75:103235. [PMID: 38889622 PMCID: PMC11231598 DOI: 10.1016/j.redox.2024.103235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Myofibroblasts are key cellular effectors of corneal wound healing from trauma, surgery, or infection. However, their persistent deposition of disorganized extracellular matrix can also cause corneal fibrosis and visual impairment. Recent work showed that the PPARγ agonist Troglitazone can mitigate established corneal fibrosis, and parallel in vitro data suggested this occurred through inhibition of the mitochondrial pyruvate carrier (MPC) rather than PPARγ. In addition to oxidative phosphorylation (Ox-Phos), pyruvate and other mitochondrial metabolites provide carbon for the synthesis of biological macromolecules. However, it is currently unclear how these roles selectively impact fibrosis. Here, we performed bioenergetic, metabolomic, and epigenetic analyses of corneal fibroblasts treated with TGF-β1 to stimulate myofibroblast trans-differentiation, with further addition of Troglitazone or the MPC inhibitor UK5099, to identify MPC-dependencies that may facilitate remodeling and loss of the myofibroblast phenotype. Our results show that a shift in energy metabolism is associated with, but not sufficient to drive cellular remodeling. Metabolites whose abundances were sensitive to MPC inhibition suggest that sustained carbon influx into the Krebs' cycle is prioritized over proline synthesis to fuel collagen deposition. Furthermore, increased abundance of acetyl-CoA and increased histone H3 acetylation suggest that epigenetic mechanisms downstream of metabolic remodeling may reinforce cellular phenotypes. Overall, our results highlight a novel molecular target and metabolic vulnerability that affects myofibroblast persistence in the context of corneal wounding.
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Affiliation(s)
- Kye-Im Jeon
- Dept. Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, NY, USA
| | - Ankita Kumar
- Dept. Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, NY, USA
| | - Paul S Brookes
- Dept. Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, USA
| | - Keith Nehrke
- Dept. Medicine-Nephrology Division, University of Rochester, Rochester, NY, USA
| | - Krystel R Huxlin
- Dept. Ophthalmology, Flaum Eye Institute and Center for Visual Science, University of Rochester, Rochester, NY, USA.
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Zhang X, Wang Y, Li H, Wang DW, Chen C. Insights into the post-translational modifications in heart failure. Ageing Res Rev 2024; 100:102467. [PMID: 39187021 DOI: 10.1016/j.arr.2024.102467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 08/01/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Heart failure (HF), as the terminal manifestation of multiple cardiovascular diseases, causes a huge socioeconomic burden worldwide. Despite the advances in drugs and medical-assisted devices, the prognosis of HF remains poor. HF is well-accepted as a myriad of subcellular dys-synchrony related to detrimental structural and functional remodelling of cardiac components, including cardiomyocytes, fibroblasts, endothelial cells and macrophages. Through the covalent chemical process, post-translational modifications (PTMs) can coordinate protein functions, such as re-localizing cellular proteins, marking proteins for degradation, inducing interactions with other proteins and tuning enzyme activities, to participate in the progress of HF. Phosphorylation, acetylation, and ubiquitination predominate in the currently reported PTMs. In addition, advanced HF is commonly accompanied by metabolic remodelling including enhanced glycolysis. Thus, glycosylation induced by disturbed energy supply is also important. In this review, firstly, we addressed the main types of HF. Then, considering that PTMs are associated with subcellular locations, we summarized the leading regulation mechanisms in organelles of distinctive cell types of different types of HF, respectively. Subsequently, we outlined the aforementioned four PTMs of key proteins and signaling sites in HF. Finally, we discussed the perspectives of PTMs for potential therapeutic targets in HF.
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Affiliation(s)
- Xudong Zhang
- Division of Cardiology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 1095# Jiefang Ave, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Yan Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 1095# Jiefang Ave, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 1095# Jiefang Ave, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 1095# Jiefang Ave, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 1095# Jiefang Ave, Wuhan 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China.
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Nasuhidehnavi A, Zarzycka W, Górecki I, Chiao YA, Lee CF. Emerging interactions between mitochondria and NAD + metabolism in cardiometabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00191-7. [PMID: 39198117 DOI: 10.1016/j.tem.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 09/01/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme for redox reactions and regulates cellular catabolic pathways. An intertwined relationship exists between NAD+ and mitochondria, with consequences for mitochondrial function. Dysregulation in NAD+ homeostasis can lead to impaired energetics and increased oxidative stress, contributing to the pathogenesis of cardiometabolic diseases. In this review, we explore how disruptions in NAD+ homeostasis impact mitochondrial function in various cardiometabolic diseases. We discuss emerging studies demonstrating that enhancing NAD+ synthesis or inhibiting its consumption can ameliorate complications of this family of pathological conditions. Additionally, we highlight the potential role and therapeutic promise of mitochondrial NAD+ transporters in regulating cellular and mitochondrial NAD+ homeostasis.
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Affiliation(s)
- Azadeh Nasuhidehnavi
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13790, USA
| | - Weronika Zarzycka
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ignacy Górecki
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ying Ann Chiao
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Chi Fung Lee
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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12
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Álvarez-González E, Sierra LM. Tricarboxylic Acid Cycle Relationships with Non-Metabolic Processes: A Short Story with DNA Repair and Its Consequences on Cancer Therapy Resistance. Int J Mol Sci 2024; 25:9054. [PMID: 39201738 PMCID: PMC11355010 DOI: 10.3390/ijms25169054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Metabolic changes involving the tricarboxylic acid (TCA) cycle have been linked to different non-metabolic cell processes. Among them, apart from cancer and immunity, emerges the DNA damage response (DDR) and specifically DNA damage repair. The oncometabolites succinate, fumarate and 2-hydroxyglutarate (2HG) increase reactive oxygen species levels and create pseudohypoxia conditions that induce DNA damage and/or inhibit DNA repair. Additionally, by influencing DDR modulation, they establish direct relationships with DNA repair on at least four different pathways. The AlkB pathway deals with the removal of N-alkylation DNA and RNA damage that is inhibited by fumarate and 2HG. The MGMT pathway acts in the removal of O-alkylation DNA damage, and it is inhibited by the silencing of the MGMT gene promoter by 2HG and succinate. The other two pathways deal with the repair of double-strand breaks (DSBs) but with opposite effects: the FH pathway, which uses fumarate to help with the repair of this damage, and the chromatin remodeling pathway, in which oncometabolites inhibit its repair by impairing the homologous recombination repair (HRR) system. Since oncometabolites inhibit DNA repair, their removal from tumor cells will not always generate a positive response in cancer therapy. In fact, their presence contributes to longer survival and/or sensitization against tumor therapy in some cancer patients.
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Affiliation(s)
- Enol Álvarez-González
- Departamento de Biología Funcional, Área de Genética, University of Oviedo, C/Julián Clavería s/n, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Avda. HUCA s/n, 33011 Oviedo, Spain
| | - Luisa María Sierra
- Departamento de Biología Funcional, Área de Genética, University of Oviedo, C/Julián Clavería s/n, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Avda. HUCA s/n, 33011 Oviedo, Spain
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13
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Cai J, Deng Y, Min Z, Li C, Zhao Z, Jing D. Deciphering the dynamics: Exploring the impact of mechanical forces on histone acetylation. FASEB J 2024; 38:e23849. [PMID: 39096133 DOI: 10.1096/fj.202400907rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/01/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024]
Abstract
Living cells navigate a complex landscape of mechanical cues that influence their behavior and fate, originating from both internal and external sources. At the molecular level, the translation of these physical stimuli into cellular responses relies on the intricate coordination of mechanosensors and transducers, ultimately impacting chromatin compaction and gene expression. Notably, epigenetic modifications on histone tails govern the accessibility of gene-regulatory sites, thereby regulating gene expression. Among these modifications, histone acetylation emerges as particularly responsive to the mechanical microenvironment, exerting significant control over cellular activities. However, the precise role of histone acetylation in mechanosensing and transduction remains elusive due to the complexity of the acetylation network. To address this gap, our aim is to systematically explore the key regulators of histone acetylation and their multifaceted roles in response to biomechanical stimuli. In this review, we initially introduce the ubiquitous force experienced by cells and then explore the dynamic alterations in histone acetylation and its associated co-factors, including HDACs, HATs, and acetyl-CoA, in response to these biomechanical cues. Furthermore, we delve into the intricate interactions between histone acetylation and mechanosensors/mechanotransducers, offering a comprehensive analysis. Ultimately, this review aims to provide a holistic understanding of the nuanced interplay between histone acetylation and mechanical forces within an academic framework.
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Affiliation(s)
- Jingyi Cai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yudi Deng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ziyang Min
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chaoyuan Li
- Department of Implantology, School and Hospital of Stomatology, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Tongji University, Shanghai, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dian Jing
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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14
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Zhang X, Lu M, An H. Lysine acetylproteome analysis reveals the lysine acetylation in developing fruit and a key acetylated protein involved in sucrose accumulation in Rosa roxburghii Tratt. J Proteomics 2024; 305:105248. [PMID: 38964538 DOI: 10.1016/j.jprot.2024.105248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Lysine acetylation is a common post-translational modification of proteins in plants. Rosa roxburghii Tratt. is an economically important fruit tree known for its high nutritional value. However, the characteristics of acetylome-related proteins during fruit development in this crop remain unknown. This study aimed to explore the global acetylproteome of R. roxburghii fruit to identify key lysine-acetylated proteins associated with its quality traits. A total of 4280 acetylated proteins were identified, among them, 981 proteins exhibited differential acetylation (DA) while 19 proteins showed increased acetylation level consistently on individual sites. Functional classification revealed that these DA proteins were primarily associated with central metabolic pathways, carbohydrate metabolism, terpenoids and polyketides metabolism, lipid metabolism, and amino acid metabolism, highlighting the importance of lysine acetylation in fruit quality formation. Notably, the most significant up-regulated acetylation occurred in sucrose synthase (SuS1), a key enzyme in sucrose biosynthesis. Enzyme assays, RNA-seq and proteome analysis indicated that SuS activity, which was independent of its transcriptome and proteome level, may be enhanced by up-acetylation, ultimately increasing sucrose accumulation. Thus, these findings offer a better understanding of the global acetylproteome of R. roxburghii fruit, while also uncover a novel mechanism of acetylated SuS-mediated in sucrose metabolism in plant. SIGNIFICANCE: Rosa roxburghii Tratt. is an important horticultural crop whose commercial value is closely linked to its fruit quality. Acetylation modification is a post-translational mechanism observed in plants, which regulates the physiological functions and metabolic fluxes involved in various biological processes. The regulatory mechanism of lysine acetylation in the fruit quality formation in perennial woody plants has not been fully elucidated, while most of the research has primarily focused on annual crops. Therefore, this study, for the first time, uses Rosaceae fruits as the research material to elucidate the regulatory role of lysine-acetylated proteins in fruit development, identify key metabolic processes influencing fruit quality formation, and provide valuable insights for cultivation strategies.
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Affiliation(s)
- Xue Zhang
- College of Forestry, Guizhou University, Guiyang 550025, China; Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, China
| | - Min Lu
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, China
| | - Huaming An
- College of Forestry, Guizhou University, Guiyang 550025, China; Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, China.
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15
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Guo Z, Zhang Y, Wang H, Liao L, Ma L, Zhao Y, Yang R, Li X, Niu J, Chu Q, Fu Y, Li B, Yang C. Hypoxia-induced downregulation of PGK1 crotonylation promotes tumorigenesis by coordinating glycolysis and the TCA cycle. Nat Commun 2024; 15:6915. [PMID: 39134530 PMCID: PMC11319824 DOI: 10.1038/s41467-024-51232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Protein post-translational modifications (PTMs) are crucial for cancer cells to adapt to hypoxia; however, the functional significance of lysine crotonylation (Kcr) in hypoxia remains unclear. Herein we report a quantitative proteomics analysis of global crotonylome under normoxia and hypoxia, and demonstrate 128 Kcr site alterations across 101 proteins in MDA-MB231 cells. Specifically, we observe a significant decrease in K131cr, K156cr and K220cr of phosphoglycerate kinase 1 (PGK1) upon hypoxia. Enoyl-CoA hydratase 1 (ECHS1) is upregulated and interacts with PGK1, leading to the downregulation of PGK1 Kcr under hypoxia. Abolishment of PGK1 Kcr promotes glycolysis and suppresses mitochondrial pyruvate metabolism by activating pyruvate dehydrogenase kinase 1 (PDHK1). A low PGK1 K131cr level is correlated with malignancy and poor prognosis of breast cancer. Our findings show that PGK1 Kcr is a signal in coordinating glycolysis and the tricarboxylic acid (TCA) cycle and may serve as a diagnostic indicator for breast cancer.
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Affiliation(s)
- Zihao Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yang Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Haoyue Wang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Liming Liao
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
| | - Lingdi Ma
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yiliang Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Ronghui Yang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xuexue Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Jing Niu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Qiaoyun Chu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yanxia Fu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Binghui Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
- Department of Cancer Cell Biology and National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
| | - Chuanzhen Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
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16
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Malanchuk O, Bdzhola A, Palchevskyi S, Bdzhola V, Chai P, Pardo OE, Seckl MJ, Banerjee A, Peak-Chew SY, Skehel M, Guruprasad L, Zhyvoloup A, Gout I, Filonenko V. Investigating the Regulation of Ribosomal Protein S6 Kinase 1 by CoAlation. Int J Mol Sci 2024; 25:8747. [PMID: 39201434 PMCID: PMC11354579 DOI: 10.3390/ijms25168747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
Ribosomal protein S6 kinases belong to a family of highly conserved enzymes in eukaryotes that regulate cell growth, proliferation, survival, and the stress response. It is well established that the activation and downstream signalling of p70S6Ks involve multiple phosphorylation events by key regulators of cell growth, survival, and energy metabolism. Here, we report for the first time the covalent modification of p70S6K1 by coenzyme A (CoA) in response to oxidative stress, which regulates its kinase activity. The site of CoA binding (CoAlation) was mapped by mass spectrometry to cysteine 217 (Cys217), located in the kinase activation loop and only one amino acid away from the tripeptide DFG motif, which facilitates ATP-binding. The CoAlation of recombinant p70S6K1 was demonstrated in vitro and was shown to inhibit its kinase activity. Our molecular docking and dynamics analysis revealed the most likely mode for CoA binding to p70S6K1. This mechanism involves the non-covalent binding of the CoA ADP moiety to the p70S6K1 nucleotide-binding pocket, positioning the CoA thiol group in close proximity to form a covalent bond with the surface-exposed Cys217 residue. These findings support a "dual anchor" mechanism for protein kinase inhibition by CoAlation in cellular response to oxidative stress. Furthermore, the inhibition of S6K1 by CoAlation may open new avenues for developing novel inhibitors.
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Affiliation(s)
- Oksana Malanchuk
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (O.M.); (A.Z.)
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
| | - Anna Bdzhola
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
| | - Sergii Palchevskyi
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
| | - Volodymyr Bdzhola
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
| | - Peng Chai
- Division of Cancer, Imperial College London, Du Cane Road, London W12 0NN, UK; (P.C.); (O.E.P.); (M.J.S.)
| | - Olivier E. Pardo
- Division of Cancer, Imperial College London, Du Cane Road, London W12 0NN, UK; (P.C.); (O.E.P.); (M.J.S.)
| | - Michael J. Seckl
- Division of Cancer, Imperial College London, Du Cane Road, London W12 0NN, UK; (P.C.); (O.E.P.); (M.J.S.)
| | - Adrija Banerjee
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India; (A.B.); (L.G.)
| | - Sew Yeu Peak-Chew
- Biological Mass Spectrometry & Proteomics Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Trumpington, Cambridge CB2 0QH, UK;
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
| | - Lalitha Guruprasad
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India; (A.B.); (L.G.)
| | - Alexander Zhyvoloup
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (O.M.); (A.Z.)
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (O.M.); (A.Z.)
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
| | - Valeriy Filonenko
- Department of Cell Signalling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine; (A.B.); (S.P.); (V.B.)
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17
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Zhou Y, Wu F, Wu J, Overmans S, Ye M, Xiao M, Peng B, Xu L, Huang J, Lu Y, Wang Y, Liang S, Zhang H, Liang X, Zhong Z, Liu H, Ruan Z, Xia J, Jin P. The adaptive mechanisms of the marine diatom Thalassiosira weissflogii to long-term high CO 2 and warming. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2001-2020. [PMID: 38943614 DOI: 10.1111/tpj.16905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
While it is known that increased dissolved CO2 concentrations and rising sea surface temperature (ocean warming) can act interactively on marine phytoplankton, the ultimate molecular mechanisms underlying this interaction on a long-term evolutionary scale are relatively unexplored. Here, we performed transcriptomics and quantitative metabolomics analyses, along with a physiological trait analysis, on the marine diatom Thalassiosira weissflogii adapted for approximately 3.5 years to warming and/or high CO2 conditions. We show that long-term warming has more pronounced impacts than elevated CO2 on gene expression, resulting in a greater number of differentially expressed genes (DEGs). The largest number of DEGs was observed in populations adapted to warming + high CO2, indicating a potential synergistic interaction between these factors. We further identified the metabolic pathways in which the DEGs function and the metabolites with significantly changed abundances. We found that ribosome biosynthesis-related pathways were upregulated to meet the increased material and energy demands after warming or warming in combination with high CO2. This resulted in the upregulation of energy metabolism pathways such as glycolysis, photorespiration, the tricarboxylic acid cycle, and the oxidative pentose phosphate pathway, as well as the associated metabolites. These metabolic changes help compensate for reduced photochemical efficiency and photosynthesis. Our study emphasizes that the upregulation of ribosome biosynthesis plays an essential role in facilitating the adaptation of phytoplankton to global ocean changes and elucidates the interactive effects of warming and high CO2 on the adaptation of marine phytoplankton in the context of global change.
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Affiliation(s)
- Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Fenghuang Wu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiao Wu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Sebastian Overmans
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Baoyi Peng
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Leyao Xu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yipeng Wang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Hao Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiao Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Zhirong Zhong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Haobin Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Zuoxi Ruan
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
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18
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Paiva I, Seguin J, Grgurina I, Singh AK, Cosquer B, Plassard D, Tzeplaeff L, Le Gras S, Cotellessa L, Decraene C, Gambi J, Alcala-Vida R, Eswaramoorthy M, Buée L, Cassel JC, Giacobini P, Blum D, Merienne K, Kundu TK, Boutillier AL. Dysregulated expression of cholesterol biosynthetic genes in Alzheimer's disease alters epigenomic signatures of hippocampal neurons. Neurobiol Dis 2024; 198:106538. [PMID: 38789057 DOI: 10.1016/j.nbd.2024.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Aging is the main risk factor of cognitive neurodegenerative diseases such as Alzheimer's disease, with epigenome alterations as a contributing factor. Here, we compared transcriptomic/epigenomic changes in the hippocampus, modified by aging and by tauopathy, an AD-related feature. We show that the cholesterol biosynthesis pathway is severely impaired in hippocampal neurons of tauopathic but not of aged mice pointing to vulnerability of these neurons in the disease. At the epigenomic level, histone hyperacetylation was observed at neuronal enhancers associated with glutamatergic regulations only in the tauopathy. Lastly, a treatment of tau mice with the CSP-TTK21 epi-drug that restored expression of key cholesterol biosynthesis genes counteracted hyperacetylation at neuronal enhancers and restored object memory. As acetyl-CoA is the primary substrate of both pathways, these data suggest that the rate of the cholesterol biosynthesis in hippocampal neurons may trigger epigenetic-driven changes, that may compromise the functions of hippocampal neurons in pathological conditions.
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Affiliation(s)
- Isabel Paiva
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
| | - Jonathan Seguin
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Iris Grgurina
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Akash Kumar Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Brigitte Cosquer
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Damien Plassard
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Laura Tzeplaeff
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Stephanie Le Gras
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Ludovica Cotellessa
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - Charles Decraene
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Johanne Gambi
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Rafael Alcala-Vida
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Muthusamy Eswaramoorthy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Jean-Christophe Cassel
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Paolo Giacobini
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - David Blum
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Karine Merienne
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Anne-Laurence Boutillier
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
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19
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Aktay I, Billur D, Tuncay E, Turan B. An Overexpression of SLC30A6 Gene Contributes to Cardiomyocyte Dysfunction via Affecting Mitochondria and Inducing Activations in K-Acetylation and Epigenetic Proteins. Biochem Genet 2024; 62:3198-3214. [PMID: 38091184 DOI: 10.1007/s10528-023-10602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/13/2023] [Indexed: 07/31/2024]
Abstract
Intracellular free Zn2+ ([Zn2+]i) is less than 1-nM in cardiomyocytes and its regulation is performed with Zn2+-transporters. However, the roles of Zn2+-transporters in cardiomyocytes are not defined exactly yet. Here, we aimed to examine the role of an overexpression and subcellular localization of a ZnT6 in insulin-resistance mimic H9c2 cardiomyoblasts (IR-cells; 50-μM palmitic acid for 24-h incubation). We used both IR-cells and ZnT6-overexpressed (ZnT6OE) cells in comparison to those of H9c2 cells (CON-cells). The IR-cells have higher ZnT6-protein levels than CON-cells while this level was similar to those of ZnT6OE-cells. The [Zn2+]i in IR-cells was increased significantly and mitochondrial localization of ZnT6 was demonstrated in these cells by using confocal microscopy visualization. Furthermore, electron microscopy analysis demonstrated abnormal morphological appearance in both IR-cells and ZnT6OE-cells characterized by irregular mitochondrion cristae and condensed and dilated cisterna in the sarcoplasmic reticulum. Mitochondria were similarly depolarized in both IR-cells and ZnT6OE-cells. The protein expression level of a mitofusin protein MFN2 in the IR-cells was decreased, significantly, whereas, it was found significantly upregulated in both ZnT6-OE-cells and IR-incubated ZnT6OE-cells, which demonstrates the role of ZnT6-overexpression but not IR. Additionally, the total protein level of a mitochondrial fission protein, dynamin-related protein 1, DRP1 was found to be increased over 1.5-fold in IR-cells while this increase was found to be higher in the ZnT6OE-cells than those of IR-cells, demonstrating an additional effect on IR-increase. ZnT6-overexpression induced also significant increases in K-acetylation, trimethylation of histone H3 lysine27, and mono-methylation of histone H3 lysine36, in a similar manner to those of IR-cells. Overall, our data point out an important contribution of ZnT6-overexpression to IR-induced cellular changes, such as alteration in mitochondria function and activation of epigenetic modifications.
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Affiliation(s)
- Irem Aktay
- Department of Biophysics, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Deniz Billur
- Department of Histology & Embryology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Erkan Tuncay
- Department of Biophysics, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Belma Turan
- Department of Biophysics, Faculty of Medicine, Lokman Hekim University, Ankara, Turkey.
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20
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Xia L, Li M, Chen Y, Dai Y, Li H, Zhang S. Sexually dimorphic acetyl-CoA biosynthesis and utilization in response to drought and exogenous acetic acid. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1967-1985. [PMID: 38944754 DOI: 10.1111/tpj.16901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/19/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Female willows exhibit greater drought tolerance and benefit more from exogenous acetic acid (AA)-improved drought tolerance than males. However, the potential mechanisms driving these sex-specific responses remain unclear. To comprehensively investigate the sexually dimorphic responsive mechanisms of willows to drought and exogenous AA, here, we performed physiological, proteomic, Lys-acetylproteomic, and transgenic analyses in female and male Salix myrtillacea exposed to drought and AA-applicated drought treatments, focusing on protein abundance and lysine acetylation (LysAc) changes. Drought-tolerant females suffered less drought-induced photosynthetic and oxidative damage, did not activate AA and acetyl-CoA biosynthesis, TCA cycle, fatty acid metabolism, and jasmonic acid signaling as strongly as drought-sensitive males. Exogenous AA caused overaccumulation of endogenous AA and inhibition of acetyl-CoA biosynthesis and utilization in males. However, exogenous AA greatly enhanced acetyl-CoA biosynthesis and utilization and further enhanced drought performance of females, possibly determining that AA improved drought tolerance more in females than in males. Interestingly, overexpression of acetyl-CoA synthetase (ACS) could reprogram fatty acids, increase LysAc levels, and improve drought tolerance, highlighting the involvement of ACS-derived acetyl-CoA in drought responses. In addition, drought and exogenous AA induced sexually dimorphic LysAc associated with histones, transcription factors, and metabolic enzymes in willows. Especially, exogenous AA may greatly improve the photosynthetic capacity of S. myrtillacea males by decreasing LysAc levels and increasing the abundances of photosynthetic proteins. While hyperacetylation in glycolysis, TCA cycle, and fatty acid biosynthesis potentially possibly serve as negative feedback to acclimate acetyl-CoA biosynthesis and utilization in drought-stressed males and AA-applicated females. Thus, acetyl-CoA biosynthesis and utilization determine the sexually dimorphic responses of S. myrtillacea to drought and exogenous AA.
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Affiliation(s)
- Linchao Xia
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Menghan Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Chen
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yujie Dai
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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21
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Han X, Qin H, Lu Y, Chen H, Yuan Z, Zhang Y, Yang X, Zheng L, Yan S. Post-translational modifications: The potential ways for killing cancer stem cells. Heliyon 2024; 10:e34015. [PMID: 39092260 PMCID: PMC11292267 DOI: 10.1016/j.heliyon.2024.e34015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
While strides in cancer treatment continue to advance, the enduring challenges posed by cancer metastasis and recurrence persist as formidable contributors to the elevated mortality rates observed in cancer patients. Among the multifaceted factors implicated in tumor recurrence and metastasis, cancer stem cells (CSCs) emerge as noteworthy entities due to their inherent resistance to conventional therapies and heightened invasive capacities. Characterized by their notable abilities for self-renewal, differentiation, and initiation of tumorigenesis, the eradication of CSCs emerges as a paramount objective. Recent investigations increasingly emphasize the pivotal role of post-translational protein modifications (PTMs) in governing the self-renewal and replication capabilities of CSCs. This review accentuates the critical significance of several prevalent PTMs and the intricate interplay of PTM crosstalk in regulating CSC behavior. Furthermore, it posits that the manipulation of PTMs may offer a novel avenue for targeting and eliminating CSC populations, presenting a compelling perspective on cancer therapeutics with substantial potential for future applications.
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Affiliation(s)
- Xuedan Han
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Hai Qin
- Department of Clinical Laboratory, Beijing Jishuitan Hospital Guizhou Hospital, No. 206, Sixian Street, Baiyun District, Guiyang City, 550014, Guizhou Province, China
| | - Yu Lu
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Haitao Chen
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Zhengdong Yuan
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Yiwen Zhang
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Xuena Yang
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China
| | - Simin Yan
- Department of Pharmacy, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
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22
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Yan E, Tan M, Jiao N, He L, Wan B, Zhang X, Yin J. Lysine 2-hydroxyisobutyrylation levels determined adipogenesis and fat accumulation in adipose tissue in pigs. J Anim Sci Biotechnol 2024; 15:99. [PMID: 38992763 PMCID: PMC11242017 DOI: 10.1186/s40104-024-01058-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Excessive backfat deposition lowering carcass grade is a major concern in the pig industry, especially in most breeds of obese type pigs. The mechanisms involved in adipogenesis and fat accumulation in pigs remain unclear. Lysine 2-hydroxyisobutyrylation (Khib), is a novel protein post-translational modification (PTM), which play an important role in transcription, energy metabolism and metastasis of cancer cells, but its role in adipogenesis and fat accumulation has not been shown. RESULTS In this study, we first analyzed the modification levels of acetylation (Kac), Khib, crotonylation (Kcr) and succinylation (Ksu) of fibro-adipogenic progenitors (FAPs), myogenic precursors (Myo) and mesenchymal stem cells (MSCs) with varied differentiation potential, and found that only Khib modification in FAPs was significantly higher than that in MSCs. Consistently, in parallel with its regulatory enzymes lysine acetyltransferase 5 (KAT5) and histone deacetylase 2 (HDAC2) protein levels, the Khib levels increased quadratically (P < 0.01) during adipogenic differentiation of FAPs. KAT5 knockdown in FAPs inhibited adipogenic differentiation, while HDAC2 knockdown enhanced adipogenic differentiation. We also demonstrated that Khib modification favored to adipogenic differentiation and fat accumulation by comparing Khib levels in FAPs and backfat tissues both derived from obese-type pigs (Laiwu pigs) and lean-type pigs (Duroc pigs), respectively. Accordingly, the expression patterns of KAT5 and HDAC2 matched well to the degree of backfat accumulation in obese- and lean-type pigs. CONCLUSIONS From the perspective of protein translational modification, we are the first to reveal the role of Khib in adipogenesis and fat deposition in pigs, and provided new clues for the improvement of fat accumulation and distribution as expected via genetic selection and nutritional strategy in obese-type pigs.
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Affiliation(s)
- Enfa Yan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingyang Tan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ning Jiao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, 271018, Shandong Province, China
| | - Linjuan He
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Boyang Wan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Molecular Design Breeding Frontier Science Center of the Ministry of Education (MOE), Beijing, 100193, China.
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Molecular Design Breeding Frontier Science Center of the Ministry of Education (MOE), Beijing, 100193, China.
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23
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Chang YC, Gnann C, Steimbach RR, Bayer FP, Lechner S, Sakhteman A, Abele M, Zecha J, Trendel J, The M, Lundberg E, Miller AK, Kuster B. Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics. Cell Rep 2024; 43:114272. [PMID: 38795348 DOI: 10.1016/j.celrep.2024.114272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/12/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024] Open
Abstract
Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.
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Affiliation(s)
- Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Christian Gnann
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; Biosciences Faculty, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Miriam Abele
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Baden-Württemberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany; German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany.
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24
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Schwab SK, Harris PS, Michel C, McGinnis CD, Nahomi RB, Assiri MA, Reisdorph R, Henriksen K, Orlicky DJ, Levi M, Rosenberg A, Nagaraj RH, Fritz KS. Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue. Proteomics Clin Appl 2024:e202400018. [PMID: 38923810 DOI: 10.1002/prca.202400018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
PURPOSE Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end-stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post-translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism. EXPERIMENTAL DESIGN A novel extraction and LC-MS/MS approach was adapted to quantify sites of lysine acetylation from formalin-fixed paraffin-embedded (FFPE) kidney tissue and from patients with DKD and non-diabetic donors (n = 5 and n = 7, respectively). RESULTS Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis. CONCLUSIONS AND CLINICAL RELEVANCE A quantitative acetylomics platform was developed for protein biomarker discovery in formalin-fixed and paraffin-embedded biopsies of kidney transplant patients suffering from DKD.
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Affiliation(s)
- Stefanie K Schwab
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Peter S Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cole Michel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Courtney D McGinnis
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rooban B Nahomi
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mohammed A Assiri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Richard Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kammi Henriksen
- Department of Pathology, University of Chicago Medical Center, Chicago, Illinois, USA
| | - David J Orlicky
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Avi Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ram H Nagaraj
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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25
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Aldehoff AS, Karkossa I, Goerdeler C, Krieg L, Schor J, Engelmann B, Wabitsch M, Landgraf K, Hackermüller J, Körner A, Rolle-Kampczyk U, Schubert K, von Bergen M. Unveiling the dynamics of acetylation and phosphorylation in SGBS and 3T3-L1 adipogenesis. iScience 2024; 27:109711. [PMID: 38840842 PMCID: PMC11152682 DOI: 10.1016/j.isci.2024.109711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/11/2023] [Accepted: 04/06/2024] [Indexed: 06/07/2024] Open
Abstract
Obesity, characterized by enlarged and dysfunctional adipose tissue, is among today's most pressing global public health challenges with continuously increasing prevalence. Despite the importance of post-translational protein modifications (PTMs) in cellular signaling, knowledge of their impact on adipogenesis remains limited. Here, we studied the temporal dynamics of transcriptome, proteome, central carbon metabolites, and the acetyl- and phosphoproteome during adipogenesis using LC-MS/MS combined with PTM enrichment strategies on human (SGBS) and mouse (3T3-L1) adipocyte models. Both cell lines exhibited unique PTM profiles during adipogenesis, with acetylated proteins being enriched for central energy metabolism, while phosphorylated proteins related to insulin signaling and organization of cellular structures. As candidates with strong correlation to the adipogenesis timeline we identified CD44 and the acetylation sites FASN_K673 and IDH_K272. While results generally aligned between SGBS and 3T3-L1 cells, details appeared cell line specific. Our datasets on SGBS and 3T3-L1 adipogenesis dynamics are accessible for further mining.
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Affiliation(s)
- Alix Sarah Aldehoff
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Cornelius Goerdeler
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Laura Krieg
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Jana Schor
- Department of Computational Biology and Chemistry, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, University Hospital for Children and Adolescents Ulm, Ulm, Germany
| | - Kathrin Landgraf
- University Hospital for Children and Adolescents, Center for Pediatric Research, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Jörg Hackermüller
- Department of Computational Biology and Chemistry, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- University Hospital for Children and Adolescents, Center for Pediatric Research, Medical Faculty, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic Obesity and Vascular Research (HI-MAG) of the Helmholtz-Centre Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
- LIFE–Leipzig Research Center for Civilization Diseases, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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26
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Liu M, Gong F, Yu W, Cao K, Xu H, Zhou X. The Rhododendron Chrysanthum Pall.s' Acetylation Modification of Rubisco Enzymes Controls Carbon Cycling to Withstand UV-B Stress. Biomolecules 2024; 14:732. [PMID: 38927135 PMCID: PMC11201758 DOI: 10.3390/biom14060732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Lysine acetylation of proteins plays a critical regulatory function in plants. A few advances have been made in the study of plant acetylproteome. However, until now, there have been few data on Rhododendron chrysanthum Pall. (R. chrysanthum). We analyzed the molecular mechanisms of photosynthesis and stress resistance in R. chrysanthum under UV-B stress. We measured chlorophyll fluorescence parameters of R. chrysanthum under UV-B stress and performed a multi-omics analysis. Based on the determination of chlorophyll fluorescence parameters, R. chrysanthum Y(NO) (Quantum yield of non-photochemical quenching) increased under UV-B stress, indicating that the plant was damaged and photosynthesis decreased. In the analysis of acetylated proteomics data, acetylated proteins were found to be involved in a variety of biological processes. Notably, acetylated proteins were significantly enriched in the pathways of photosynthesis and carbon fixation, suggesting that lysine acetylation modifications have an important role in these activities. Our findings suggest that R. chrysanthum has decreased photosynthesis and impaired photosystems under UV-B stress, but NPQ shows that plants are resistant to UV-B. Acetylation proteomics revealed that up- or down-regulation of acetylation modification levels alters protein expression. Acetylation modification of key enzymes of the Calvin cycle (Rubisco, GAPDH) regulates protein expression, making Rubisco and GAPDH proteins expressed as significantly different proteins, which in turn affects the carbon fixation capacity of R. chrysanthum. Thus, Rubisco and GAPDH are significantly differentially expressed after acetylation modification, which affects the carbon fixation capacity and thus makes the plant resistant to UV-B stress. Lysine acetylation modification affects biological processes by regulating the expression of key enzymes in photosynthesis and carbon fixation, making plants resistant to UV-B stress.
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Affiliation(s)
| | | | | | | | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
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27
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Ito M, Nishida Y, Iwamoto T, Kanai A, Aoyama S, Ueki K, Uzawa H, Iida H, Watada H. Protein acylations induced by a ketogenic diet demonstrate diverse patterns depending on organs and differ between histones and global proteins. Biochem Biophys Res Commun 2024; 712-713:149960. [PMID: 38640734 DOI: 10.1016/j.bbrc.2024.149960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
An essential ketone body, β-hydroxybutyrate (BOHB), plays various roles in physiological regulations via protein acylations such as lysine acetylation and β-hydroxybutyrylation. Here, to understand how BOHB systemically regulates acylations from an overarching perspective, we administered a ketogenic diet to mice to increase BOHB concentration and examined acylations. We found that global acetylation and β-hydroxybutyrylation dramatically increase in various organs except for the brains, where the increase was much smaller than in the other organs. Interestingly, we observe no increase in histone acetylation in the organs where significant global protein acetylation occurs despite a substantial rise in histone β-hydroxybutyrylation. Finally, we compared the transcriptome data of the mice's liver after the ketogenic diet to the public databases, showing that upregulated genes are enriched in those related to histone β-hydroxybutyrylation in starvation. Our data indicate that a ketogenic diet induces diverse patterns of acylations depending on organs and protein localizations, suggesting that different mechanisms regulate acylations and that the ketogenic diet is associated with starvation in terms of protein modifications.
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Affiliation(s)
- Minami Ito
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuya Nishida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Tatsuya Iwamoto
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Akiko Kanai
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shuhei Aoyama
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyosei Ueki
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotsugu Uzawa
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hitoshi Iida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotaka Watada
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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Liebner T, Kilic S, Walter J, Aibara H, Narita T, Choudhary C. Acetylation of histones and non-histone proteins is not a mere consequence of ongoing transcription. Nat Commun 2024; 15:4962. [PMID: 38862536 PMCID: PMC11166988 DOI: 10.1038/s41467-024-49370-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
In all eukaryotes, acetylation of histone lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of transcription is debated. One model suggests that transcription promotes the recruitment and/or activation of acetyltransferases, and histone acetylation occurs as a consequence of ongoing transcription. However, the extent to which transcription shapes the global protein acetylation landscapes is not known. Here, we show that global protein acetylation remains virtually unaltered after acute transcription inhibition. Transcription inhibition ablates the co-transcriptionally occurring ubiquitylation of H2BK120 but does not reduce histone acetylation. The combined inhibition of transcription and CBP/p300 further demonstrates that acetyltransferases remain active and continue to acetylate histones independently of transcription. Together, these results show that histone acetylation is not a mere consequence of transcription; acetyltransferase recruitment and activation are uncoupled from the act of transcription, and histone and non-histone protein acetylation are sustained in the absence of ongoing transcription.
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Affiliation(s)
- Tim Liebner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Sinan Kilic
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jonas Walter
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Hitoshi Aibara
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Takeo Narita
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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Meyer GA, Ferey JLA, Sanford JA, Fitzgerald LS, Greenberg AE, Svensson K, Greenberg MJ, Schenk S. Insights into posttranslational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP. J Appl Physiol (1985) 2024; 136:1559-1567. [PMID: 38722753 PMCID: PMC11365544 DOI: 10.1152/japplphysiol.00156.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
Mice with skeletal muscle-specific and inducible double knockout of the lysine acetyltransferases, p300 (E1A binding protein p300) and CBP (cAMP-response element-binding protein binding protein), referred to as i-mPCKO, demonstrate a dramatic loss of contractile function in skeletal muscle and ultimately die within 7 days. Given that many proteins involved in ATP generation and cross-bridge cycling are acetylated, we investigated whether these processes are dysregulated in skeletal muscle from i-mPCKO mice and, thus, whether they could underlie the rapid loss of muscle contractile function. Just 4-5 days after inducing knockout of p300 and CBP in skeletal muscle from adult i-mPCKO mice, there was ∼90% reduction in ex vivo contractile function in the extensor digitorum longus (EDL) and a ∼65% reduction in in vivo ankle dorsiflexion torque, as compared with wild type (WT; i.e., Cre negative) littermates. Despite this profound loss of contractile force in i-mPCKO mice, there were no genotype-driven differences in fatigability during repeated contractions, nor were there genotype differences in mitochondrial-specific pathway enrichment of the proteome, intermyofibrillar mitochondrial volume, or mitochondrial respiratory function. As it relates to cross-bridge cycling, remarkably, the overt loss of contractile function in i-mPCKO muscle was reversed in permeabilized fibers supplied with exogenous Ca2+ and ATP, with active tension being similar between i-mPCKO and WT mice, regardless of Ca2+ concentration. Actin-myosin motility was also similar in skeletal muscle from i-mPCKO and WT mice. In conclusion, neither mitochondrial abundance/function, nor actomyosin cross-bridge cycling, are the underlying driver of contractile dysfunction in i-mPCKO mice.NEW & NOTEWORTHY The mechanism underlying dramatic loss of muscle contractile function with inducible deletion of both E1A binding protein p300 (p300) and cAMP-response element-binding protein binding protein (CBP) in skeletal muscle remains unknown. Here, we find that impairments in mitochondrial function or cross-bridge cycling are not the underlying mechanism of action. Future work will investigate other aspects of excitation-contraction coupling, such as Ca2+ handling and membrane excitability, as contractile function could be rescued by permeabilizing skeletal muscle, which provides exogenous Ca2+ and bypasses membrane depolarization.
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Affiliation(s)
- Gretchen A Meyer
- Program in Physical Therapy, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Jeremie L A Ferey
- Program in Physical Therapy, Washington University School of Medicine, St. Louis, Missouri, United States
| | - James A Sanford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Liam S Fitzgerald
- Department of Orthopaedic Surgery, School of Medicine, University of California San Diego, San Diego, California, United States
- Biomedical Sciences Graduate Program, School of Medicine, University of California San Diego, San Diego, California, United States
- Medical Scientist Training Program, School of Medicine, University of California San Diego, San Diego, California, United States
| | - Akiva E Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Kristoffer Svensson
- Department of Orthopaedic Surgery, School of Medicine, University of California San Diego, San Diego, California, United States
| | - Michael J Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Simon Schenk
- Department of Orthopaedic Surgery, School of Medicine, University of California San Diego, San Diego, California, United States
- Biomedical Sciences Graduate Program, School of Medicine, University of California San Diego, San Diego, California, United States
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30
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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31
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Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem 2024; 16:913-921. [PMID: 38531969 PMCID: PMC11164685 DOI: 10.1038/s41557-024-01500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to -1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein-DNA and protein-protein interactions in biological processes from replication to ubiquitin signalling.
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Affiliation(s)
- Maria Weyh
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marie-Lena Jokisch
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tuan-Anh Nguyen
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maximilian Fottner
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Kathrin Lang
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany.
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32
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Waykar TR, Mandlik SK, Mandlik DS. Sirtuins: exploring next-gen therapeutics in the pathogenesis osteoporosis and associated diseases. Immunopharmacol Immunotoxicol 2024; 46:277-301. [PMID: 38318808 DOI: 10.1080/08923973.2024.2315418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
OBJECTIVE Osteoporosis poses a substantial public health challenge due to an ageing population and the lack of adequate treatment options. The condition is marked by a reduction in bone mineral density, resulting in an elevated risk of fractures. The reduction in bone density and strength, as well as musculoskeletal issues that come with aging, present a significant challenge for individuals impacted by these conditions, as well as the healthcare system worldwide. METHODS Literature survey was conducted until May 2023 using databases such as Web of Science, PubMed, Scopus, and Google Scholar. RESULT Sirtuins 1-7 (SIRT1-SIRT7), which are a group of Nicotinamide adenine dinucleotide (NAD+)-dependent deacetylases, possess remarkable capabilities to increase lifespan and combat diseases related to aging. Research has demonstrated that these proteins play an important role in regular skeletal development and maintenance by directly impacting bone cells. Their dysfunction could be a factor in various bone conditions. Studies conducted on animals before clinical trials have shown that administering Sirtuins agonists to mice provides a safeguard against osteoporosis resulting from aging, menopause, and immobilization. These findings imply that Sirtuins may be a viable target for addressing the irregularity in bone remodeling and treating osteoporosis and other skeletal ailments. CONCLUSION The purpose of this review was to present a thorough and current evaluation of the existing knowledge on Sirtuins biology, with a particular emphasis on their involvement in maintaining bone homeostasis and contributing to osteoporosis. Additionally, the review examines potential pharmacological interventions targeting Sirtuins for the treatment of osteoporosis.
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Affiliation(s)
- Tejal R Waykar
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Satish K Mandlik
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Deepa S Mandlik
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, India
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33
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Mailloux RJ. The emerging importance of the α-keto acid dehydrogenase complexes in serving as intracellular and intercellular signaling platforms for the regulation of metabolism. Redox Biol 2024; 72:103155. [PMID: 38615490 PMCID: PMC11021975 DOI: 10.1016/j.redox.2024.103155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024] Open
Abstract
The α-keto acid dehydrogenase complex (KDHc) class of mitochondrial enzymes is composed of four members: pyruvate dehydrogenase (PDHc), α-ketoglutarate dehydrogenase (KGDHc), branched-chain keto acid dehydrogenase (BCKDHc), and 2-oxoadipate dehydrogenase (OADHc). These enzyme complexes occupy critical metabolic intersections that connect monosaccharide, amino acid, and fatty acid metabolism to Krebs cycle flux and oxidative phosphorylation (OxPhos). This feature also imbues KDHc enzymes with the heightened capacity to serve as platforms for propagation of intracellular and intercellular signaling. KDHc enzymes serve as a source and sink for mitochondrial hydrogen peroxide (mtH2O2), a vital second messenger used to trigger oxidative eustress pathways. Notably, deactivation of KDHc enzymes through reversible oxidation by mtH2O2 and other electrophiles modulates the availability of several Krebs cycle intermediates and related metabolites which serve as powerful intracellular and intercellular messengers. The KDHc enzymes also play important roles in the modulation of mitochondrial metabolism and epigenetic programming in the nucleus through the provision of various acyl-CoAs, which are used to acylate proteinaceous lysine residues. Intriguingly, nucleosomal control by acylation is also achieved through PDHc and KGDHc localization to the nuclear lumen. In this review, I discuss emerging concepts in the signaling roles fulfilled by the KDHc complexes. I highlight their vital function in serving as mitochondrial redox sensors and how this function can be used by cells to regulate the availability of critical metabolites required in cell signaling. Coupled with this, I describe in detail how defects in KDHc function can cause disease states through the disruption of cell redox homeodynamics and the deregulation of metabolic signaling. Finally, I propose that the intracellular and intercellular signaling functions of the KDHc enzymes are controlled through the reversible redox modification of the vicinal lipoic acid thiols in the E2 subunit of the complexes.
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Affiliation(s)
- Ryan J Mailloux
- School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.
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34
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Danková D, Olsen CA. Reversing the charge of lysine by genetic code expansion. Nat Chem 2024; 16:849-851. [PMID: 38831035 DOI: 10.1038/s41557-024-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Affiliation(s)
- Daniela Danková
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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35
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Bhattacharya S, Tu BP. Histone acylation at a glance. J Cell Sci 2024; 137:jcs261250. [PMID: 38842578 PMCID: PMC11213524 DOI: 10.1242/jcs.261250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
An important mechanism of gene expression regulation is the epigenetic modification of histones. The cofactors and substrates for these modifications are often intermediary metabolites, and it is becoming increasingly clear that the metabolic and nutritional state of cells can influence these marks. These connections between the balance of metabolites, histone modifications and downstream transcriptional changes comprise a metabolic signaling program that can enable cells to adapt to changes in nutrient availability. Beyond acetylation, there is evidence now that histones can be modified by other acyl groups. In this Cell Science at a Glance article and the accompanying poster, we focus on these histone acylation modifications and provide an overview of the players that govern these acylations and their connections with metabolism.
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Affiliation(s)
- Saikat Bhattacharya
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Benjamin P. Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
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36
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Scherer NM, Maurel C, Graus M, McAlary L, Richter G, Radford RW, Hogan A, Don E, Lee A, Yerbury J, Francois M, Chung R, Morsch M. RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo. Nucleic Acids Res 2024; 52:5301-5319. [PMID: 38381071 PMCID: PMC11109982 DOI: 10.1093/nar/gkae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Insoluble cytoplasmic aggregate formation of the RNA-binding protein TDP-43 is a major hallmark of neurodegenerative diseases including Amyotrophic Lateral Sclerosis. TDP-43 localizes predominantly in the nucleus, arranging itself into dynamic condensates through liquid-liquid phase separation (LLPS). Mutations and post-translational modifications can alter the condensation properties of TDP-43, contributing to the transition of liquid-like biomolecular condensates into solid-like aggregates. However, to date it has been a challenge to study the dynamics of this process in vivo. We demonstrate through live imaging that human TDP-43 undergoes nuclear condensation in spinal motor neurons in a living animal. RNA-binding deficiencies as well as post-translational modifications can lead to aberrant condensation and altered TDP-43 compartmentalization. Single-molecule tracking revealed an altered mobility profile for RNA-binding deficient TDP-43. Overall, these results provide a critically needed in vivo characterization of TDP-43 condensation, demonstrate phase separation as an important regulatory mechanism of TDP-43 accessibility, and identify a molecular mechanism of how functional TDP-43 can be regulated.
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Affiliation(s)
- Natalie M Scherer
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Cindy Maurel
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Matthew S Graus
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Grant Richter
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Rowan A W Radford
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Alison Hogan
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily K Don
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Justin Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Mathias Francois
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Roger S Chung
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Marco Morsch
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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37
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Keenan EK, Bareja A, Lam Y, Grimsrud PA, Hirschey MD. Cysteine S-acetylation is a post-translational modification involved in metabolic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595030. [PMID: 38826225 PMCID: PMC11142221 DOI: 10.1101/2024.05.21.595030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cysteine is a reactive amino acid central to the catalytic activities of many enzymes. It is also a common target of post-translational modifications (PTMs), such as palmitoylation. This longchain acyl PTM can modify cysteine residues and induce changes in protein subcellular localization. We hypothesized that cysteine could also be modified by short-chain acyl groups, such as cysteine S-acetylation. To test this, we developed sample preparation and non-targeted mass spectrometry protocols to analyze the mouse liver proteome for cysteine acetylation. Our findings revealed hundreds of sites of cysteine acetylation across multiple tissue types, revealing a previously uncharacterized cysteine acetylome. Cysteine acetylation shows a marked cytoplasmic subcellular localization signature, with tissue-specific acetylome patterns and specific changes upon metabolic stress. This study uncovers a novel aspect of cysteine biochemistry, highlighting short-chain modifications alongside known long-chain acyl PTMs. These findings enrich our understanding of the landscape of acyl modifications and suggest new research directions in enzyme activity regulation and cellular signaling in metabolism.
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Affiliation(s)
- E. Keith Keenan
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham NC 27701
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham NC 27710
| | - Akshay Bareja
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham NC 27701
- Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University, Medical Center, Durham NC 27710
| | - Yannie Lam
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham NC 27701
| | - Paul A. Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham NC 27701
- Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University, Medical Center, Durham NC 27710
| | - Matthew D. Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham NC 27701
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham NC 27710
- Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University, Medical Center, Durham NC 27710
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38
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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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Rogina B, Tissenbaum HA. SIRT1, resveratrol and aging. Front Genet 2024; 15:1393181. [PMID: 38784035 PMCID: PMC11112063 DOI: 10.3389/fgene.2024.1393181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Aging is linked to a time-associated decline in both cellular function and repair capacity leading to malfunction on an organismal level, increased frailty, higher incidence of diseases, and death. As the population grows older, there is a need to reveal mechanisms associated with aging that could spearhead treatments to postpone the onset of age-associated decline, extend both healthspan and lifespan. One possibility is targeting the sirtuin SIRT1, the founding member of the sirtuin family, a highly conserved family of histone deacetylases that have been linked to metabolism, stress response, protein synthesis, genomic instability, neurodegeneration, DNA damage repair, and inflammation. Importantly, sirtuins have also been implicated to promote health and lifespan extension, while their dysregulation has been linked to cancer, neurological processes, and heart disorders. SIRT1 is one of seven members of sirtuin family; each requiring nicotinamide adenine dinucleotide (NAD+) as co-substrate for their catalytic activity. Overexpression of yeast, worm, fly, and mice SIRT1 homologs extend lifespan in each animal, respectively. Moreover, lifespan extension due to calorie restriction are associated with increased sirtuin activity. These findings led to the search for a calorie restriction mimetic, which revealed the compound resveratrol; (3, 5, 4'-trihydroxy-trans-stilbene) belonging to the stilbenoids group of polyphenols. Following this finding, resveratrol and other sirtuin-activating compounds have been extensively studied for their ability to affect health and lifespan in a variety of species, including humans via clinical studies.
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Affiliation(s)
- Blanka Rogina
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
- Institute for Systems Genomics, Farmington, CT, United States
| | - Heidi A. Tissenbaum
- Department of Molecular, Cell and Cancer Biology UMass Chan Medical School, Worcester, MA, United States
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Liu M, Sun L, Cao Y, Xu H, Zhou X. Acetylation proteomics and metabolomics analyses reveal the involvement of starch synthase undergoing acetylation modification during UV-B stress resistance in Rhododendron Chrysanthum Pall. Hereditas 2024; 161:15. [PMID: 38702800 PMCID: PMC11067277 DOI: 10.1186/s41065-024-00320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Rhododendron chrysanthum Pall. (R. chrysanthum) is a plant that lives in high mountain with strong UV-B radiation, so R. chrysanthum possess resistance to UV-B radiation. The process of stress resistance in plants is closely related to metabolism. Lysine acetylation is an important post-translational modification, and this modification process is involved in a variety of biological processes, and affected the expression of enzymes in metabolic processes. However, little is known about acetylation proteomics during UV-B stress resistance in R. chrysanthum. RESULTS In this study, R. chrysanthum OJIP curves indicated that UV-B stress damaged the receptor side of the PSII reaction center, with a decrease in photosynthesis, a decrease in sucrose content and an increase in starch content. A total of 807 differentially expressed proteins, 685 differentially acetylated proteins and 945 acetylation sites were identified by quantitative proteomic and acetylation modification histological analysis. According to COG and subcellular location analyses, DEPs with post-translational modification of proteins and carbohydrate metabolism had important roles in resistance to UV-B stress and DEPs were concentrated in chloroplasts. KEGG analyses showed that DEPs were enriched in starch and sucrose metabolic pathways. Analysis of acetylation modification histology showed that the enzymes in the starch and sucrose metabolic pathways underwent acetylation modification and the modification levels were up-regulated. Further analysis showed that only GBSS and SSGBSS changed to DEPs after undergoing acetylation modification. Metabolomics analyses showed that the metabolite content of starch and sucrose metabolism in R. chrysanthum under UV-B stress. CONCLUSIONS Decreased photosynthesis in R. chrysanthum under UV-B stress, which in turn affects starch and sucrose metabolism. In starch synthesis, GBSS undergoes acetylation modification and the level is upregulated, promotes starch synthesis, making R. chrysanthum resistant to UV-B stress.
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Affiliation(s)
- Meiqi Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, China
| | - Li Sun
- Siping Central People's Hospital, Siping, China
| | - Yuhang Cao
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, China
| | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, China
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, China.
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Mubaid S, Sanchez BJ, Algehani RA, Skopenkova V, Adjibade P, Hall DT, Busque S, Lian XJ, Ashour K, Tremblay AMK, Carlile G, Gagné JP, Diaz-Gaxiola A, Khattak S, Di Marco S, Thomas DY, Poirier GG, Gallouzi IE. Tankyrase-1 regulates RBP-mediated mRNA turnover to promote muscle fiber formation. Nucleic Acids Res 2024; 52:4002-4020. [PMID: 38321934 DOI: 10.1093/nar/gkae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Poly(ADP-ribosylation) (PARylation) is a post-translational modification mediated by a subset of ADP-ribosyl transferases (ARTs). Although PARylation-inhibition based therapies are considered as an avenue to combat debilitating diseases such as cancer and myopathies, the role of this modification in physiological processes such as cell differentiation remains unclear. Here, we show that Tankyrase1 (TNKS1), a PARylating ART, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration. Although all bona fide PARPs are expressed in muscle cells, experiments using siRNA-mediated knockdown or pharmacological inhibition show that TNKS1 is the enzyme responsible of catalyzing PARylation during myogenesis. Via this activity, TNKS1 controls the turnover of mRNAs encoding myogenic regulatory factors such as nucleophosmin (NPM) and myogenin. TNKS1 mediates these effects by targeting RNA-binding proteins such as Human Antigen R (HuR). HuR harbors a conserved TNKS-binding motif (TBM), the mutation of which not only prevents the association of HuR with TNKS1 and its PARylation, but also precludes HuR from regulating the turnover of NPM and myogenin mRNAs as well as from promoting myogenesis. Therefore, our data uncover a new role for TNKS1 as a key modulator of RBP-mediated post-transcriptional events required for vital processes such as myogenesis.
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Affiliation(s)
- Souad Mubaid
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Brenda Janice Sanchez
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Rinad A Algehani
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Viktoriia Skopenkova
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Pauline Adjibade
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Derek T Hall
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Sandrine Busque
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Xian Jin Lian
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Kholoud Ashour
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Anne-Marie K Tremblay
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - Graeme Carlile
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Andrea Diaz-Gaxiola
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Shahryar Khattak
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
| | - David Y Thomas
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - Imed-Eddine Gallouzi
- KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Dept. of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, 1160 Pine Avenue, Montreal, QC H3A 1A3, Canada
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Dashti P, Lewallen EA, Gordon JAR, Montecino MA, Davie JR, Stein GS, van Leeuwen JPTM, van der Eerden BCJ, van Wijnen AJ. Epigenetic regulators controlling osteogenic lineage commitment and bone formation. Bone 2024; 181:117043. [PMID: 38341164 DOI: 10.1016/j.bone.2024.117043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bone formation and homeostasis are controlled by environmental factors and endocrine regulatory cues that initiate intracellular signaling pathways capable of modulating gene expression in the nucleus. Bone-related gene expression is controlled by nucleosome-based chromatin architecture that limits the accessibility of lineage-specific gene regulatory DNA sequences and sequence-specific transcription factors. From a developmental perspective, bone-specific gene expression must be suppressed during the early stages of embryogenesis to prevent the premature mineralization of skeletal elements during fetal growth in utero. Hence, bone formation is initially inhibited by gene suppressive epigenetic regulators, while other epigenetic regulators actively support osteoblast differentiation. Prominent epigenetic regulators that stimulate or attenuate osteogenesis include lysine methyl transferases (e.g., EZH2, SMYD2, SUV420H2), lysine deacetylases (e.g., HDAC1, HDAC3, HDAC4, HDAC7, SIRT1, SIRT3), arginine methyl transferases (e.g., PRMT1, PRMT4/CARM1, PRMT5), dioxygenases (e.g., TET2), bromodomain proteins (e.g., BRD2, BRD4) and chromodomain proteins (e.g., CBX1, CBX2, CBX5). This narrative review provides a broad overview of the covalent modifications of DNA and histone proteins that involve hundreds of enzymes that add, read, or delete these epigenetic modifications that are relevant for self-renewal and differentiation of mesenchymal stem cells, skeletal stem cells and osteoblasts during osteogenesis.
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Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada; CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada.
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | | | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Andre J van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
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Han J, Wang L, Tang X, Liu R, Shi L, Zhu J, Zhao M. Glsirt1-mediated deacetylation of GlCAT regulates intracellular ROS levels, affecting ganoderic acid biosynthesis in Ganoderma lucidum. Free Radic Biol Med 2024; 216:1-11. [PMID: 38458391 DOI: 10.1016/j.freeradbiomed.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. However, in Basidiomycetes, the extent of lysine acetylation of nonhistone proteins remains largely unknown. Recently, we identified the deacetylase Glsirt1 as a key regulator of the biosynthesis of ganoderic acid (GA), a key secondary metabolite of Ganoderma lucidum. To gain insight into the characteristics, extent, and biological function of Glsirt1-mediated lysine acetylation in G. lucidum, we aimed to identify additional Glsirt1 substrates via comparison of acetylomes between wild-type (WT) and Glsirt1-silenced mutants. A large amount of Glsirt1-dependent lysine acetylation occurs in G. lucidum according to the results of this omics analysis, involving energy metabolism, protein synthesis, the stress response and other pathways. Our results suggest that GlCAT is a direct target of Glsirt1 and that the deacetylation of GlCAT by Glsirt1 reduces catalase activity, thereby leading to the accumulation of intracellular reactive oxygen species (ROS) and positively regulating the biosynthesis of GA. Our findings provide evidence for the involvement of nonhistone lysine acetylation in the biological processes of G. lucidum and help elucidate the involvement of important ROS signaling molecules in regulating physiological and biochemical processes in this organism. In conclusion, this proteomic analysis reveals a striking breadth of cellular processes affected by lysine acetylation and provides new nodes of intervention in the biosynthesis of secondary metabolites in G. lucidum.
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Affiliation(s)
- Jing Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Lingshuai Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Xin Tang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Rui Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
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Long Y, Zhao Z, Xie W, Shi J, Yang F, Zhu D, Jiang P, Tang Q, Ti Z, Jiang B, Yang X, Gao G, Qi W. Kallistatin leads to cognition impairment via downregulating glutamine synthetase. Pharmacol Res 2024; 202:107145. [PMID: 38492829 DOI: 10.1016/j.phrs.2024.107145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
In many neurodegenerative disorders, such as Alzheimer's disease (AD), glutamate-mediated neuronal excitotoxicity is considered the basis for cognitive impairment. The mRNA and protein expression of SERPINA4(Kallistatin) are higher in patients with AD. However, whether Kallistatin plays a regulatory role in glutamate-glutamine cycle homeostasis remains unclear. In this study, we identified impaired cognitive function in Kallistatin transgenic (KAL-TG) mice. Baseline glutamate levels were elevated and miniature excitatory postsynaptic current (mEPSC) frequency was increased in the hippocampus, suggesting the impairment of glutamate homeostasis in KAL-TG mice. Mechanistically, we demonstrated that Kallistatin promoted lysine acetylation and ubiquitination of glutamine synthetase (GS) and facilitated its degradation via the proteasome pathway, thereby downregulating GS. Fenofibrate improved cognitive memory in KAL-TG mice by downregulating serum Kallistatin. Collectively, our study findings provide insights the mechanism by which Kallistatin regulates cognitive impairment, and suggest the potential of fenofibrate to prevente and treat of AD patients with high levels of Kallistatin.
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Affiliation(s)
- Yanlan Long
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhen Zhao
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wanting Xie
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinhui Shi
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fengyu Yang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Dan Zhu
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Jiang
- Department of Clinical Medical Laboratory, Guangzhou First People Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qilong Tang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhou Ti
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bin Jiang
- Guangdong Province Key Laboratory of Brain Function and Disease, School of Medicine, Sun Yat-sen University, Shenzhen, China.
| | - Xia Yang
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Guoquan Gao
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; China Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China; Guangdong Provincial Key Laboratory of Diabetology, Guangzhou, Guangdong, China.
| | - Weiwei Qi
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Guangdong Engineering & Technology Research Center for Gene Manipulation and Biomacromolecular Products (Sun Yat-sen University), Guangzhou, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, China.
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Wang T, Zou Y, Meng H, Zheng P, Teng J, Huang N, Chen J. Securin acetylation prevents precocious separase activation and premature sister chromatid separation. Curr Biol 2024; 34:1295-1308.e5. [PMID: 38452759 DOI: 10.1016/j.cub.2024.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Lysine acetylation of non-histone proteins plays crucial roles in many cellular processes. In this study, we examine the role of lysine acetylation during sister chromatid separation in mitosis. We investigate the acetylation of securin at K21 by cell-cycle-dependent acetylome analysis and uncover its role in separase-triggered chromosome segregation during mitosis. Prior to the onset of anaphase, the acetylated securin via TIP60 prevents its degradation by the APC/CCDC20-mediated ubiquitin-proteasome system. This, in turn, restrains precocious activation of separase and premature separation of sister chromatids. Additionally, the acetylation-dependent stability of securin is also enhanced by its dephosphorylation. As anaphase approaches, HDAC1-mediated deacetylation of securin promotes its degradation, allowing released separase to cleave centromeric cohesin. Blocking securin deacetylation leads to longer anaphase duration and errors in chromosome segregation. Thus, this study illustrates the emerging role of securin acetylation dynamics in mitotic progression and genetic stability.
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Affiliation(s)
- Tianning Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Breast Disease Diagnosis and Treatment Center/Department of Thyroid Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China; Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Yuhong Zou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Meng
- Institute of Neuroscience, Translational Medicine Institute, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Pengli Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Ning Huang
- Institute of Neuroscience, Translational Medicine Institute, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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Yuan Y, Li P, Li J, Zhao Q, Chang Y, He X. Protein lipidation in health and disease: molecular basis, physiological function and pathological implication. Signal Transduct Target Ther 2024; 9:60. [PMID: 38485938 PMCID: PMC10940682 DOI: 10.1038/s41392-024-01759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 03/18/2024] Open
Abstract
Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.
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Affiliation(s)
- Yuan Yuan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Li
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianghui Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Xingxing He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
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Mozzetta C, Sartorelli V, Steinkuhler C, Puri PL. HDAC inhibitors as pharmacological treatment for Duchenne muscular dystrophy: a discovery journey from bench to patients. Trends Mol Med 2024; 30:278-294. [PMID: 38408879 PMCID: PMC11095976 DOI: 10.1016/j.molmed.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Earlier evidence that targeting the balance between histone acetyltransferases (HATs) and deacetylases (HDACs), through exposure to HDAC inhibitors (HDACis), could enhance skeletal myogenesis, prompted interest in using HDACis to promote muscle regeneration. Further identification of constitutive HDAC activation in dystrophin-deficient muscles, caused by dysregulated nitric oxide (NO) signaling, provided the rationale for HDACi-based therapeutic interventions for Duchenne muscular dystrophy (DMD). In this review, we describe the molecular, preclinical, and clinical evidence supporting the efficacy of HDACis in countering disease progression by targeting pathogenic networks of gene expression in multiple muscle-resident cell types of patients with DMD. Given that givinostat is paving the way for HDACi-based interventions in DMD, next-generation HDACis with optimized therapeutic profiles and efficacy could be also explored for synergistic combinations with other therapeutic strategies.
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Affiliation(s)
- Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Rome, Italy
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Pier Lorenzo Puri
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Meyer GA, Ferey JLA, Sanford JA, Fitzgerald LS, Greenberg AE, Svensson K, Greenberg MJ, Schenk S. Insights into post-translational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582179. [PMID: 38463996 PMCID: PMC10925228 DOI: 10.1101/2024.02.27.582179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mice with skeletal muscle-specific inducible double knockout of the lysine acetyltransferases, p300 (E1A binding protein p300) and CBP (cAMP-response element-binding protein binding protein), referred to as i-mPCKO, demonstrate a dramatic loss of contractile function in skeletal muscle and ultimately die within 7 days. Given that many proteins involved in ATP generation and cross-bridge cycling are acetylated, we investigated whether these processes are dysregulated in skeletal muscle from i-mPCKO mice and thus could underlie the rapid loss of muscle contractile function. Just 4-5 days after inducing knockout of p300 and CBP in skeletal muscle from adult i-mPCKO mice, there was ∼90% reduction in ex vivo contractile function in the extensor digitorum longus (EDL) and a ∼65% reduction in in vivo ankle dorsiflexion torque, as compared to wildtype (WT; i.e. Cre negative) littermates. Despite the profound loss of contractile force in i-mPCKO mice, there were no genotype-driven differences in fatigability during repeated contractions, nor were there genotype differences in mitochondrial specific pathway enrichment of the proteome, intermyofibrillar mitochondrial volume or mitochondrial respiratory function. As it relates to cross-bridge cycling, remarkably, the overt loss of contractile function in i-mPCKO muscle was reversed in permeabilized fibers supplied with exogenous Ca 2+ and ATP, with active tension being similar between i-mPCKO and WT mice, regardless of Ca 2+ concentration. Actin-myosin motility was also similar in skeletal muscle from i-mPCKO and WT mice. In conclusion, neither mitochondrial abundance/function, nor actomyosin cross-bridge cycling, are the underlying driver of contractile dysfunction in i-mPCKO mice. New & Noteworthy The mechanism underlying dramatic loss of muscle contractile function with inducible deletion of both p300 and CBP in skeletal muscle remains unknown. Here we find that impairments in mitochondrial function or cross-bridge cycling are not the underlying mechanism of action. Future work will investigate other aspects of excitation-contraction coupling, such as Ca 2+ handling and membrane excitability, as contractile function could be rescued by permeabilizing skeletal muscle, which provides exogenous Ca 2+ and bypasses membrane depolarization.
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Shi J, Lv Q, Miao D, Xiong Z, Wei Z, Wu S, Tan D, Wang K, Zhang X. HIF2α Promotes Cancer Metastasis through TCF7L2-Dependent Fatty Acid Synthesis in ccRCC. RESEARCH (WASHINGTON, D.C.) 2024; 7:0322. [PMID: 38390305 PMCID: PMC10882601 DOI: 10.34133/research.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Recent studies have highlighted the notable involvement of the crosstalk between hypoxia-inducible factor 2 alpha (HIF2α) and Wnt signaling components in tumorigenesis. However, the cellular function and precise regulatory mechanisms of HIF2α and Wnt signaling interactions in clear cell renal cell carcinoma (ccRCC) remain elusive. To analyze the correlation between HIF2α and Wnt signaling, we utilized the Cancer Genome Atlas - Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) public database, HIF2α RNA sequencing data, and conducted luciferase reporter assays. A Wnt-related gene set was employed to identify key regulators of Wnt signaling controlled by HIF2α in ccRCC. Furthermore, we assessed the biological effects of TCF7L2 on ccRCC metastasis and lipid metabolism in both in vivo and in vitro settings. Our outcomes confirm TCF7L2 as a key gene involved in HIF2α-mediated regulation of the canonical Wnt pathway. Functional studies demonstrate that TCF7L2 promotes metastasis in ccRCC. Mechanistic investigations reveal that HIF2α stabilizes TCF7L2 mRNA in a method based on m6A by transcriptionally regulating METTL3. Up-regulation of TCF7L2 enhances cellular fatty acid oxidation, which promotes histone acetylation. This facilitates the transcription of genes connected to epithelial-mesenchymal transition and ultimately enhances metastasis of ccRCC. These outcomes offer a novel understanding into the involvement of lipid metabolism in the signaling pathway regulation, offering valuable implications for targeted treatment in ccRCC.
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Affiliation(s)
- Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Qingyang Lv
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Daojia Miao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Zhihao Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Songming Wu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Diaoyi Tan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Keshan Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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