1
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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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2
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Zhang R, Liu S, Mousavi SM. Cognitive Dysfunction and Exercise: From Epigenetic to Genetic Molecular Mechanisms. Mol Neurobiol 2024:10.1007/s12035-024-03970-7. [PMID: 38286967 DOI: 10.1007/s12035-024-03970-7] [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: 11/16/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024]
Abstract
Maintaining good health is crucial, and exercise plays a vital role in achieving this goal. It offers a range of positive benefits for cognitive function, regardless of age. However, as our population ages and life expectancy increases, cognitive impairment has become a prevalent issue, often coexisting with age-related neurodegenerative conditions. This can result in devastating consequences such as memory loss, difficulty speaking, and confusion, greatly hindering one's ability to lead an ordinary life. In addition, the decrease in mental capacity has a significant effect on an individual's physical and emotional well-being, greatly reducing their overall level of contentment and causing a significant financial burden for communities. While most current approaches aim to slow the decline of cognition, exercise offers a non-pharmacological, safe, and accessible solution. Its effects on cognition are intricate and involve changes in the brain's neural plasticity, mitochondrial stability, and energy metabolism. Moreover, exercise triggers the release of cytokines, playing a significant role in the body-brain connection and its impact on cognition. Additionally, exercise can influence gene expression through epigenetic mechanisms, leading to lasting improvements in brain function and behavior. Herein, we summarized various genetic and epigenetic mechanisms that can be modulated by exercise in cognitive dysfunction.
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Affiliation(s)
- Runhong Zhang
- Department of Physical Education, Luliang University, Lishi, 033000, Shanxi, China.
| | - Shangwu Liu
- Department of Physical Education, Luliang University, Lishi, 033000, Shanxi, China
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3
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Wang M, Zhu Q, Yao N, Liang W, Ma X, Li J, Li X, Wang L, Liang W. The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress. Int J Mol Sci 2023; 24:ijms24098446. [PMID: 37176152 PMCID: PMC10179182 DOI: 10.3390/ijms24098446] [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: 03/27/2023] [Revised: 05/06/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023] Open
Abstract
Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO2 fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.
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Affiliation(s)
- Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Qiang Zhu
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Ning Yao
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Wangli Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaoxia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jingjing Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
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4
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A multi-omics analysis reveals that the lysine deacetylase ABHD14B influences glucose metabolism in mammals. J Biol Chem 2022; 298:102128. [PMID: 35700823 PMCID: PMC9270251 DOI: 10.1016/j.jbc.2022.102128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
The sirtuins and histone deacetylases are the best characterized members of the lysine deacetylase (KDAC) enzyme family. Recently, we annotated the “orphan” enzyme ABHD14B (α/β-hydrolase domain containing protein # 14B) as a novel KDAC and showed this enzyme’s ability to transfer an acetyl-group from protein lysine residue(s) to coenzyme-A to yield acetyl-coenzyme-A, thereby, expanding the repertoire of this enzyme family. However, the role of ABHD14B in metabolic processes is not fully elucidated. Here, we investigated the role of this enzyme using mammalian cell knockdowns in a combined transcriptomics and metabolomics analysis. We found from these complementary experiments in vivo that the loss of ABHD14B results in significantly altered glucose metabolism, specifically the decreased flux of glucose through glycolysis and the citric acid cycle. Further, we show that depleting hepatic ABHD14B in mice also results in defective systemic glucose metabolism, particularly during fasting. Taken together, our findings illuminate the important metabolic functions that the KDAC ABHD14B plays in mammalian physiology and poses new questions regarding the role of this hitherto cryptic metabolism-regulating enzyme.
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5
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Yang P. Editorial: Proteomics of Post-translational Modifications in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:894314. [PMID: 35712578 PMCID: PMC9195732 DOI: 10.3389/fpls.2022.894314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
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6
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Sellami M, Elrayess MA, Puce L, Bragazzi NL. Molecular Big Data in Sports Sciences: State-of-Art and Future Prospects of OMICS-Based Sports Sciences. Front Mol Biosci 2022; 8:815410. [PMID: 35087871 PMCID: PMC8787195 DOI: 10.3389/fmolb.2021.815410] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Together with environment and experience (that is to say, diet and training), the biological and genetic make-up of an athlete plays a major role in exercise physiology. Sports genomics has shown, indeed, that some DNA single nucleotide polymorphisms (SNPs) can be associated with athlete performance and level (such as elite/world-class athletic status), having an impact on physical activity behavior, endurance, strength, power, speed, flexibility, energetic expenditure, neuromuscular coordination, metabolic and cardio-respiratory fitness, among others, as well as with psychological traits. Athletic phenotype is complex and depends on the combination of different traits and characteristics: as such, it requires a “complex science,” like that of metadata and multi-OMICS profiles. Several projects and trials (like ELITE, GAMES, Gene SMART, GENESIS, and POWERGENE) are aimed at discovering genomics-based biomarkers with an adequate predictive power. Sports genomics could enable to optimize and maximize physical performance, as well as it could predict the risk of sports-related injuries. Exercise has a profound impact on proteome too. Proteomics can assess both from a qualitative and quantitative point of view the modifications induced by training. Recently, scholars have assessed the epigenetics changes in athletes. Summarizing, the different omics specialties seem to converge in a unique approach, termed sportomics or athlomics and defined as a “holistic and top-down,” “non-hypothesis-driven research on an individual’s metabolite changes during sports and exercise” (the Athlome Project Consortium and the Santorini Declaration) Not only sportomics includes metabonomics/metabolomics, but relying on the athlete’s biological passport or profile, it would enable the systematic study of sports-induced changes and effects at any level (genome, transcriptome, proteome, etc.). However, the wealth of data is so huge and massive and heterogenous that new computational algorithms and protocols are needed, more computational power is required as well as new strategies for properly and effectively combining and integrating data.
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Affiliation(s)
- Maha Sellami
- Physical Education Department, College of Education, Qatar University, Doha, Qatar
| | - Mohamed A. Elrayess
- Biomedical Research Center, Qatar University, Doha, Qatar
- QU Health, Qatar University, Doha, Qatar
| | - Luca Puce
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Nicola Luigi Bragazzi
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, ON, Canada
- Postgraduate School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Section of Musculoskeletal Disease, National Institute for Health Research (NIHR) Leeds Musculoskeletal Biomedical Research Unit, Leeds Institute of Molecular Medicine, Chapel Allerton Hospital, University of Leeds, Leeds, United Kingdom
- *Correspondence: Nicola Luigi Bragazzi,
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7
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Mu R, Ma Z, Lu C, Wang H, Cheng X, Tuo B, Fan Y, Liu X, Li T. Role of succinylation modification in thyroid cancer and breast cancer. Am J Cancer Res 2021. [PMID: 34765287 DOI: 10.2156/j.ajcr.2021.11.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The incidence of thyroid cancer and breast cancer is increasing year by year, and the specific pathogenesis is unclear. Posttranslational modifications constitute an important regulatory mechanism that affects the function of almost all proteins, are essential for a diverse and well-functioning proteome and can integrate metabolism with physiological and pathological processes. In recent years, posttranslational modifications, which mainly include metabolic enzyme-mediated protein posttranslational modifications, such as methylation, phosphorylation, acetylation and succinylation, have become a research hotspot. Among these modifications, lysine succinylation is a newly discovered broad-spectrum, dynamic, non-enzymatic protein post-translational modification, and it plays an important regulatory role in a variety of tumors. Studies have shown that succinylation can affect the synthesis of thyroid hormones, and the regulation of this post-translational modification can inhibit the apoptosis and migration of thyroid cancer cell lines, and promote breast cancer cell proliferation, DNA damage repair and autophagy-related regulation. However, the specific regulatory mechanism of succinylation in thyroid cancer and breast cancer is currently unclear. Therefore, this article mainly reviews the research progress of succinylation modification in thyroid cancer and breast cancer. It is expected to provide new directions and targets for the prevention and treatment of thyroid cancer and breast cancer.
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Affiliation(s)
- Renmin Mu
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
| | - Zhiyuan Ma
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China.,Digestive Disease Institute of Guizhou Province Zunyi 563003, Guizhou Province, China
| | - Chengli Lu
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
| | - Hu Wang
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
| | - Xiaoming Cheng
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
| | - Biguang Tuo
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China.,Digestive Disease Institute of Guizhou Province Zunyi 563003, Guizhou Province, China
| | - Yi Fan
- Endoscopy Center, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
| | - Xuemei Liu
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China.,Digestive Disease Institute of Guizhou Province Zunyi 563003, Guizhou Province, China
| | - Taolang Li
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University Zunyi 563003, Guizhou Province, China
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8
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Liu Z, Song J, Miao W, Yang B, Zhang Z, Chen W, Tan F, Suo H, Dai X, Zou X, Ou L. Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper ( Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:730489. [PMID: 34512705 PMCID: PMC8429487 DOI: 10.3389/fpls.2021.730489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the "carbon fixation in the photosynthetic organisms" pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.
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Affiliation(s)
- Zhoubin Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Jingshuang Song
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Wu Miao
- Hunan Xiangyan Seed Industry Co., Ltd, Changsha, China
| | - Bozhi Yang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Zhuqing Zhang
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Wenchao Chen
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Fangjun Tan
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Huan Suo
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xiongze Dai
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Lijun Ou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
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9
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Sun L, Bhawal R, Xu H, Chen H, Anderson ET, Haroutunian V, Cross AC, Zhang S, Gibson GE. The human brain acetylome reveals that decreased acetylation of mitochondrial proteins associates with Alzheimer's disease. J Neurochem 2021; 158:282-296. [PMID: 33905124 DOI: 10.1111/jnc.15377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/19/2021] [Indexed: 11/28/2022]
Abstract
Metabolic changes that correlate to cognitive changes are well-known in Alzheimer's disease (AD). Metabolism is often linked to functional changes in proteins by post-translational modifications. The importance of the regulation of transcription by acetylation is well documented. Advanced mass spectrometry reveals hundreds of acetylated proteins in multiple tissues, but the acetylome of human brain, its functional significance, and the changes with disease are unknown. Filling this gap is critical for understanding the pathophysiology and development of therapies. To fill this gap, we assessed the human brain acetylome in human brain and its changes with AD. More than 5% of the 4,442 proteins from the human brain global proteome were acetylated. Acetylated proteins were primarily found in the cytosol (148), mitochondria (100), nucleus (91), and plasma membrane (58). The comparison of the brain acetylome in controls to that of patients with AD revealed striking and selective differences in terms of its abundances of acetylated peptides/sites. Acetylation of 18 mitochondrial proteins decreased, while acetylation of two cytosolic proteins, tau and GFAP, increased. Our experiments demonstrate that acetylation at some specific lysine sites alters enzyme function. The results indicate that general activation of de-acetylases (i.e., sirtuins) is not an appropriate therapeutic approach for AD.
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Affiliation(s)
- Lidan Sun
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA.,Integrated Medicine Research Center for Neurological Rehabilitation, College of Medicine, Jiaxing University, Jiaxing, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Hui Xu
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Huanlian Chen
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Vahrum Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, NY, USA.,Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abigail C Cross
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Gary E Gibson
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
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10
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Moffett JR, Puthillathu N, Vengilote R, Jaworski DM, Namboodiri AM. Acetate Revisited: A Key Biomolecule at the Nexus of Metabolism, Epigenetics and Oncogenesis-Part 1: Acetyl-CoA, Acetogenesis and Acyl-CoA Short-Chain Synthetases. Front Physiol 2020; 11:580167. [PMID: 33281616 PMCID: PMC7689297 DOI: 10.3389/fphys.2020.580167] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Acetate is a major end product of bacterial fermentation of fiber in the gut. Acetate, whether derived from the diet or from fermentation in the colon, has been implicated in a range of health benefits. Acetate is also generated in and released from various tissues including the intestine and liver, and is generated within all cells by deacetylation reactions. To be utilized, all acetate, regardless of the source, must be converted to acetyl coenzyme A (acetyl-CoA), which is carried out by enzymes known as acyl-CoA short-chain synthetases. Acyl-CoA short-chain synthetase-2 (ACSS2) is present in the cytosol and nuclei of many cell types, whereas ACSS1 is mitochondrial, with greatest expression in heart, skeletal muscle, and brown adipose tissue. In addition to acting to redistribute carbon systemically like a ketone body, acetate is becoming recognized as a cellular regulatory molecule with diverse functions beyond the formation of acetyl-CoA for energy derivation and lipogenesis. Acetate acts, in part, as a metabolic sensor linking nutrient balance and cellular stress responses with gene transcription and the regulation of protein function. ACSS2 is an important task-switching component of this sensory system wherein nutrient deprivation, hypoxia and other stressors shift ACSS2 from a lipogenic role in the cytoplasm to a regulatory role in the cell nucleus. Protein acetylation is a critical post-translational modification involved in regulating cell behavior, and alterations in protein acetylation status have been linked to multiple disease states, including cancer. Improving our fundamental understanding of the "acetylome" and how acetate is generated and utilized at the subcellular level in different cell types will provide much needed insight into normal and neoplastic cellular metabolism and the epigenetic regulation of phenotypic expression under different physiological stressors. This article is Part 1 of 2 - for Part 2 see doi: 10.3389/fphys.2020.580171.
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Affiliation(s)
- John R Moffett
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Narayanan Puthillathu
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Ranjini Vengilote
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Diane M Jaworski
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT, United States
| | - Aryan M Namboodiri
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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11
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The Role of Nutri(epi)genomics in Achieving the Body's Full Potential in Physical Activity. Antioxidants (Basel) 2020; 9:antiox9060498. [PMID: 32517297 PMCID: PMC7346155 DOI: 10.3390/antiox9060498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Physical activity represents a powerful tool to achieve optimal health. The overall activation of several molecular pathways is associated with many beneficial effects, mainly converging towards a reduced systemic inflammation. Not surprisingly, regular activity can contribute to lowering the “epigenetic age”, acting as a modulator of risk toward several diseases and enhancing longevity. Behind this, there are complex molecular mechanisms induced by exercise, which modulate gene expression, also through epigenetic modifications. The exercise-induced epigenetic imprint can be transient or permanent and contributes to the muscle memory, which allows the skeletal muscle adaptation to environmental stimuli previously encountered. Nutrition, through key macro- and micronutrients with antioxidant properties, can play an important role in supporting skeletal muscle trophism and those molecular pathways triggering the beneficial effects of physical activity. Nutrients and antioxidant food components, reversibly altering the epigenetic imprint, have a big impact on the phenotype. This assigns a role of primary importance to nutri(epi)genomics, not only in optimizing physical performance, but also in promoting long term health. The crosstalk between physical activity and nutrition represents a major environmental pressure able to shape human genotypes and phenotypes, thus, choosing the right combination of lifestyle factors ensures health and longevity.
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12
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Svensson K, LaBarge SA, Sathe A, Martins VF, Tahvilian S, Cunliffe JM, Sasik R, Mahata SK, Meyer GA, Philp A, David LL, Ward SR, McCurdy CE, Aslan JE, Schenk S. p300 and cAMP response element-binding protein-binding protein in skeletal muscle homeostasis, contractile function, and survival. J Cachexia Sarcopenia Muscle 2020; 11:464-477. [PMID: 31898871 PMCID: PMC7113519 DOI: 10.1002/jcsm.12522] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/22/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Reversible ε-amino acetylation of lysine residues regulates transcription as well as metabolic flux; however, roles for specific lysine acetyltransferases in skeletal muscle physiology and function are unknown. In this study, we investigated the role of the related acetyltransferases p300 and cAMP response element-binding protein-binding protein (CBP) in skeletal muscle transcriptional homeostasis and physiology in adult mice. METHODS Mice with skeletal muscle-specific and inducible knockout of p300 and CBP (PCKO) were generated by crossing mice with a tamoxifen-inducible Cre recombinase expressed under the human α-skeletal actin promoter with mice having LoxP sites flanking exon 9 of the Ep300 and Crebbp genes. Knockout of PCKO was induced at 13-15 weeks of age via oral gavage of tamoxifen for 5 days to both PCKO and littermate control [wildtype (WT)] mice. Body composition, food intake, and muscle function were assessed on day 0 (D0) through 5 (D5). Microarray and tandem mass tag mass spectrometry analyses were performed to assess global RNA and protein levels in skeletal muscle of PCKO and WT mice. RESULTS At D5 after initiating tamoxifen treatment, there was a reduction in body weight (-15%), food intake (-78%), stride length (-46%), and grip strength (-45%) in PCKO compared with WT mice. Additionally, ex vivo contractile function [tetanic tension (kPa)] was severely impaired in PCKO vs. WT mice at D3 (~70-80% lower) and D5 (~80-95% lower) and resulted in lethality within 1 week-a phenotype that is reversed by the presence of a single allele of either p300 or CBP. The impaired muscle function in PCKO mice was paralleled by substantial transcriptional alterations (3310 genes; false discovery rate < 0.1), especially in gene networks central to muscle contraction and structural integrity. This transcriptional uncoupling was accompanied by changes in protein expression patterns indicative of impaired muscle function, albeit to a smaller magnitude (446 proteins; fold-change > 1.25; false discovery rate < 0.1). CONCLUSIONS These data reveal that p300 and CBP are required for the control and maintenance of contractile function and transcriptional homeostasis in skeletal muscle and, ultimately, organism survival. By extension, modulating p300/CBP function may hold promise for the treatment of disorders characterized by impaired contractile function in humans.
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Affiliation(s)
- Kristoffer Svensson
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Samuel A LaBarge
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Abha Sathe
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Vitor F Martins
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Shahriar Tahvilian
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA
| | - Jennifer M Cunliffe
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Roman Sasik
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil K Mahata
- VA San Diego Healthcare System, San Diego, CA, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gretchen A Meyer
- Program in Physical Therapy and Departments of Neurology, Biomedical Engineering and Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Philp
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Larry L David
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Samuel R Ward
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA.,Department of Radiology, University of California San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carrie E McCurdy
- Department of Human Physiology, University of Oregon, Eugene, OR, USA
| | - Joseph E Aslan
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA.,Knight Cardiovascular Institute, School of Medicine, Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, USA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
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13
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Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. J Comput Aided Mol Des 2020; 34:857-878. [PMID: 32180123 DOI: 10.1007/s10822-020-00304-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 03/07/2020] [Indexed: 12/30/2022]
Abstract
Valproic acid (VPA) is a compound currently used in clinical practice for the treatment of epilepsy as well as bipolar and mood disorders. VPA targets histone deacetylases (HDACs), which participate in the removal of acetyl groups from lysine in several proteins, regulating a wide variety of functions within the organism. An imbalance or malfunction of these enzymes is associated with the development and progression of several diseases, such as cancer and neurodegenerative diseases. HDACs are divided into four classes, but VPA only targets Class I (HDAC1-3 and 8) and Class IIa (HDAC4-5, 7 and 9) HDACs; however, structural and energetic information regarding the manner by which VPA inhibits these HDACs is lacking. Here, the structural and energetic features that determine this recognition were studied using molecular docking and molecular dynamics (MD) simulation. It was found that VPA reaches the catalytic site in HDAC1-3 and 7, whereas in HDAC6, VPA only reaches the catalytic tunnel. In HDAC4, VPA was bound adjacent to L1 and L2, a zone that participates in corepressor binding, and in HDAC8, VPA was bound to the hydrophobic active site channel (HASC), in line with previous reports.
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14
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Svensson K, Tahvilian S, Martins VF, Dent JR, Lemanek A, Barooni N, Greyslak K, McCurdy CE, Schenk S. Combined overexpression of SIRT1 and knockout of GCN5 in adult skeletal muscle does not affect glucose homeostasis or exercise performance in mice. Am J Physiol Endocrinol Metab 2020; 318:E145-E151. [PMID: 31794263 PMCID: PMC7052578 DOI: 10.1152/ajpendo.00370.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Sirtuin 1 (SIRT1) and general control of amino acid synthesis 5 (GCN5) regulate mitochondrial biogenesis via opposing modulation of peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) acetylation status and activity. However, the combined contribution of SIRT1 and GCN5 to skeletal muscle metabolism and endurance performance in vivo is unknown. In this study, we investigated the impact of combined skeletal muscle-specific overexpression of SIRT1 and deletion of GCN5 on glucose homeostasis, skeletal muscle mitochondrial biogenesis and function, and metabolic adaptation to endurance exercise training in mice. We generated mice with combined and tamoxifen-inducible skeletal muscle-specific overexpression of SIRT1 and knockout of GCN5 (dTG) and floxed [wild type (WT)] littermates using a Cre-LoxP approach. All mice were treated with tamoxifen at 5-6 wk of age, and 4-7 wk later glucose homeostasis, skeletal muscle contractile function, mitochondrial function, and the effects of 14 days of voluntary wheel running on expression of metabolic proteins and exercise capacity were assessed. There was no difference in oral glucose tolerance, skeletal muscle contractile function, mitochondrial abundance, or maximal respiratory capacity between dTG and WT mice. Additionally, there were no genotype differences in exercise performance and markers of mitochondrial biogenesis after 14 days of voluntary wheel running. These results demonstrate that combined overexpression of SIRT1 and loss of GCN5 in vivo does not promote metabolic remodeling in skeletal muscle of sedentary or exercise-trained mice.
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Affiliation(s)
- Kristoffer Svensson
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Shahriar Tahvilian
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Vitor F Martins
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
| | - Jessica R Dent
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Adrianna Lemanek
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Neeka Barooni
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Keenan Greyslak
- Department of Human Physiology, University of Oregon, Eugene, Oregon
| | - Carrie E McCurdy
- Department of Human Physiology, University of Oregon, Eugene, Oregon
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
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15
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Rajendran A, Vaidya K, Mendoza J, Bridwell-Rabb J, Kamat SS. Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme. Biochemistry 2019; 59:183-196. [PMID: 31478652 DOI: 10.1021/acs.biochem.9b00703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The metabolic serine hydrolase family is, arguably, one of the largest functional enzyme classes in mammals, including humans, comprising 1-2% of the total proteome. This enzyme family uses a conserved nucleophilic serine residue in the active site to perform diverse hydrolytic reactions and consists of proteases, lipases, esterases, amidases, and transacylases, which are prototypical members of this family. In humans, this enzyme family consists of >250, of which approximately 40% members remain unannotated, in terms of both their endogenous substrates and the biological pathways that they regulate. The enzyme ABHD14B, an outlying member of this family, is also known as CCG1/TAFII250-interacting factor B, as it was found to be associated with transcription initiation factor TFIID. The crystal structure of human ABHD14B was determined more than a decade ago; however, its endogenous substrates remain elusive. In this paper, we annotate ABHD14B as a lysine deacetylase (KDAC), showing this enzyme's ability to transfer an acetyl group from a post-translationally acetylated lysine to coenzyme A (CoA), to yield acetyl-CoA, while regenerating the free amine of protein lysine residues. We validate these findings by in vitro biochemical assays using recombinantly purified human ABHD14B in conjunction with cellular studies in a mammalian cell line by knocking down ABHD14B and by identification of a putative substrate binding site. Finally, we report the development and characterization of a much-needed, exquisitely selective ABHD14B antibody, and using it, we map the cellular and tissue distribution of ABHD14B and prospective metabolic pathways that this enzyme might biologically regulate.
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Affiliation(s)
- Abinaya Rajendran
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Kaveri Vaidya
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Johnny Mendoza
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Siddhesh S Kamat
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
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16
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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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17
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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18
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Dent JR, Martins VF, Svensson K, LaBarge SA, Schlenk NC, Esparza MC, Buckner EH, Meyer GA, Hamilton DL, Schenk S, Philp A. Muscle-specific knockout of general control of amino acid synthesis 5 (GCN5) does not enhance basal or endurance exercise-induced mitochondrial adaptation. Mol Metab 2017; 6:1574-1584. [PMID: 29111103 PMCID: PMC5699915 DOI: 10.1016/j.molmet.2017.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 09/29/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Lysine acetylation is an important post-translational modification that regulates metabolic function in skeletal muscle. The acetyltransferase, general control of amino acid synthesis 5 (GCN5), has been proposed as a regulator of mitochondrial biogenesis via its inhibitory action on peroxisome proliferator activated receptor-γ coactivator-1α (PGC-1α). However, the specific contribution of GCN5 to skeletal muscle metabolism and mitochondrial adaptations to endurance exercise in vivo remain to be defined. We aimed to determine whether loss of GCN5 in skeletal muscle enhances mitochondrial density and function, and the adaptive response to endurance exercise training. METHODS We used Cre-LoxP methodology to generate mice with muscle-specific knockout of GCN5 (mKO) and floxed, wildtype (WT) littermates. We measured whole-body energy expenditure, as well as markers of mitochondrial density, biogenesis, and function in skeletal muscle from sedentary mice, and mice that performed 20 days of voluntary endurance exercise training. RESULTS Despite successful knockdown of GCN5 activity in skeletal muscle of mKO mice, whole-body energy expenditure as well as skeletal muscle mitochondrial abundance and maximal respiratory capacity were comparable between mKO and WT mice. Further, there were no genotype differences in endurance exercise-mediated mitochondrial biogenesis or increases in PGC-1α protein content. CONCLUSION These results demonstrate that loss of GCN5 in vivo does not promote metabolic remodeling in mouse skeletal muscle.
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Affiliation(s)
- Jessica R Dent
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, UK
| | - Vitor F Martins
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA; Biomedical Sciences Graduate Program, University of California, La Jolla, San Diego, CA, USA
| | - Kristoffer Svensson
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Samuel A LaBarge
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Noah C Schlenk
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Mary C Esparza
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Elisa H Buckner
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Gretchen A Meyer
- Program in Physical Therapy, Washington University School of Medicine, St Louis, MO, USA
| | | | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA; Biomedical Sciences Graduate Program, University of California, La Jolla, San Diego, CA, USA.
| | - Andrew Philp
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, UK.
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19
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Alleyn M, Breitzig M, Lockey R, Kolliputi N. The dawn of succinylation: a posttranslational modification. Am J Physiol Cell Physiol 2017; 314:C228-C232. [PMID: 29167150 DOI: 10.1152/ajpcell.00148.2017] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Posttranslational modifications affect almost all proteins and are critical to a well-functioning and diverse proteome; however, many modifications remain relatively unknown and unstudied. This paper will give a perspective on the rapidly developing, novel posttranslational modification called succinylation. This modification may be implicated in numerous diseases, such as hepatic, cardiac, and pulmonary diseases. Although the influences of this modification still remain poorly understood, we are confident that further research into succinylation will provide an enhanced understanding of the complex machinery within the mitochondria, as well as the imposing consequences associated with its dysfunction.
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Affiliation(s)
- Matthew Alleyn
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Mason Breitzig
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Richard Lockey
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
| | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida , Tampa, Florida
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20
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Grazioli E, Dimauro I, Mercatelli N, Wang G, Pitsiladis Y, Di Luigi L, Caporossi D. Physical activity in the prevention of human diseases: role of epigenetic modifications. BMC Genomics 2017; 18:802. [PMID: 29143608 PMCID: PMC5688489 DOI: 10.1186/s12864-017-4193-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modification refers to heritable changes in gene function that cannot be explained by alterations in the DNA sequence. The current literature clearly demonstrates that the epigenetic response is highly dynamic and influenced by different biological and environmental factors such as aging, nutrient availability and physical exercise. As such, it is well accepted that physical activity and exercise can modulate gene expression through epigenetic alternations although the type and duration of exercise eliciting specific epigenetic effects that can result in health benefits and prevent chronic diseases remains to be determined. This review highlights the most significant findings from epigenetic studies involving physical activity/exercise interventions known to benefit chronic diseases such as metabolic syndrome, diabetes, cancer, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Elisa Grazioli
- Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy
| | - Ivan Dimauro
- Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy
| | - Guan Wang
- FIMS Reference Collaborating Centre of Sports Medicine for Anti-Doping Research, University of Brighton, Brighton, UK
| | - Yannis Pitsiladis
- Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy.,FIMS Reference Collaborating Centre of Sports Medicine for Anti-Doping Research, University of Brighton, Brighton, UK
| | - Luigi Di Luigi
- Department of Movement, Human and Health Sciences, Unit of Endocrinology, University of Rome "Foro Italico", Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, Unit of Biology, Genetics and Biochemistry, University of Rome "Foro Italico", Rome, Italy.
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21
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Palmitate-induced lipotoxicity alters acetylation of multiple proteins in clonal β cells and human pancreatic islets. Sci Rep 2017; 7:13445. [PMID: 29044173 PMCID: PMC5647430 DOI: 10.1038/s41598-017-13908-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/14/2017] [Indexed: 02/02/2023] Open
Abstract
Type 2 diabetes is characterized by progressive β cell dysfunction, with lipotoxicity playing a possible pathogenetic role. Palmitate is often used to examine the direct effects of lipotoxicity and it may cause mitochondrial alterations by activating protein acetylation. However, it is unknown whether palmitate influences protein acetylation in β cells. We investigated lysine acetylation in mitochondrial proteins from INS-1E β cells (INS-1E) and in proteins from human pancreatic islets (HPI) after 24 h palmitate exposure. First, we confirmed that palmitate damages β cells and demonstrated that chemical inhibition of deacetylation also impairs INS-1E function and survival. Then, by 2-D gel electrophoresis, Western Blot and Liquid Chromatography-Mass Spectrometry we evaluated the effects of palmitate on protein acetylation. In mitochondrial preparations from palmitate-treated INS-1E, 32 acetylated spots were detected, with 13 proteins resulting over-acetylated. In HPI, 136 acetylated proteins were found, of which 11 were over-acetylated upon culture with palmitate. Interestingly, three proteins, glutamate dehydrogenase, mitochondrial superoxide dismutase, and SREBP-1, were over-acetylated in both INS-1E and HPI. Therefore, prolonged exposure to palmitate induces changes in β cell protein lysine acetylation and this modification could play a role in causing β cell damage. Dysregulated acetylation may be a target to counteract palmitate-induced β cell lipotoxicity.
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22
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Hoffman NJ. Omics and Exercise: Global Approaches for Mapping Exercise Biological Networks. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029884. [PMID: 28348175 DOI: 10.1101/cshperspect.a029884] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The application of global "-omics" technologies to exercise has introduced new opportunities to map the complexity and interconnectedness of biological networks underlying the tissue-specific responses and systemic health benefits of exercise. This review will introduce major research tracks and recent advancements in this emerging field, as well as critical gaps in understanding the orchestration of molecular exercise dynamics that will benefit from unbiased omics investigations. Furthermore, significant research hurdles that need to be overcome to effectively fill these gaps related to data collection, computation, interpretation, and integration across omics applications will be discussed. Collectively, a cross-disciplinary physiological and omics-based systems approach will lead to discovery of a wealth of novel exercise-regulated targets for future mechanistic validation. This frontier in exercise biology will aid the development of personalized therapeutic strategies to improve athletic performance and human health through precision exercise medicine.
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Affiliation(s)
- Nolan J Hoffman
- Centre for Exercise and Nutrition, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia
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23
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Hyndman KA, Knepper MA. Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. Am J Physiol Renal Physiol 2017; 313:F842-F846. [PMID: 28701313 DOI: 10.1152/ajprenal.00313.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022] Open
Abstract
Reversible posttranslational modification of proteins is a critically important process in physiological regulation in all tissues, including the kidney. Lysine acetylation occurs in all organisms, including prokaryotes, and is regulated by a balance between the lysine acetyltransferases (adding an acetyl group to the ε-amino group of a lysine) and deacetylases (removing it). The kidney is an organ rich with acetylated lysines, which map to >2,000 unique histone and nonhistone proteins. However, the functional significance of these modifications remains to be discovered. Here, we have compiled gene lists of the acetyltransferases and deacetylases in the mammalian genomes and mapped their mRNA expression along the renal tubule. These lists will be useful for generating targeted approaches to test the physiological or pathophysiological significance of lysine acetylation changes in the kidney.
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Affiliation(s)
- Kelly A Hyndman
- Division of Nephrology, Section of Cardio-Renal Physiology and Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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24
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Broadbent J, Sampson D, Sabapathy S, Haseler LJ, Wagner KH, Bulmer AC, Peake JM, Neubauer O. Gene networks in skeletal muscle following endurance exercise are coexpressed in blood neutrophils and linked with blood inflammation markers. J Appl Physiol (1985) 2017; 122:752-766. [PMID: 28104750 DOI: 10.1152/japplphysiol.00114.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 11/22/2022] Open
Abstract
It remains incompletely understood whether there is an association between the transcriptome profiles of skeletal muscle and blood leukocytes in response to exercise or other physiological stressors. We have previously analyzed the changes in the muscle and blood neutrophil transcriptome in eight trained men before and 3, 48, and 96 h after 2 h cycling and running. Because we collected muscle and blood in the same individuals and under the same conditions, we were able to directly compare gene expression between the muscle and blood neutrophils. Applying weighted gene coexpression network analysis (WGCNA) as an advanced network-driven method to these original data sets enabled us to compare the muscle and neutrophil transcriptomes in a rigorous and systematic manner. Two gene networks were identified that were preserved between skeletal muscle and blood neutrophils, functionally related to mitochondria and posttranslational processes. Strong preservation measures (Zsummary > 10) for both muscle-neutrophil gene networks were evident within the postexercise recovery period. Muscle and neutrophil gene coexpression was strongly correlated in the mitochondria-related network (r = 0.97; P = 3.17E-2). We also identified multiple correlations between muscular gene subnetworks and exercise-induced changes in blood leukocyte counts, inflammation, and muscle damage markers. These data reveal previously unidentified gene coexpression between skeletal muscle and blood neutrophils following exercise, showing the value of WGCNA to understand exercise physiology. Furthermore, these findings provide preliminary evidence in support of the notion that blood neutrophil gene networks may potentially help us to track physiological and pathophysiological changes in the muscle.NEW & NOTEWORTHY By using weighted gene coexpression network analysis, an advanced bioinformatics method, we have identified previously unknown, functional gene networks that are preserved between skeletal muscle and blood neutrophils during recovery from exercise. These novel preliminary data suggest that muscular gene networks are coexpressed in blood leukocytes following physiological stress. This is a step forward toward the development of blood neutrophil gene subnetworks as part of blood biomarker panels to assess muscle health and disease.
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Affiliation(s)
- James Broadbent
- Tissue Repair and Translational Physiology Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Dayle Sampson
- Tissue Repair and Translational Physiology Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Surendran Sabapathy
- School of Allied Health Sciences, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Luke J Haseler
- School of Allied Health Sciences, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, Faculty of Life Sciences and Research Platform Active Ageing, University of Vienna, Vienna, Austria; and
| | - Andrew C Bulmer
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Jonathan M Peake
- Tissue Repair and Translational Physiology Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Oliver Neubauer
- Tissue Repair and Translational Physiology Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia;
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25
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Liemburg-Apers DC, Wagenaars JAL, Smeitink JAM, Willems PHGM, Koopman WJH. Acute stimulation of glucose influx upon mitoenergetic dysfunction requires LKB1, AMPK, Sirt2 and mTOR-RAPTOR. J Cell Sci 2016; 129:4411-4423. [PMID: 27793977 DOI: 10.1242/jcs.194480] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/24/2016] [Indexed: 12/20/2022] Open
Abstract
Mitochondria play a central role in cellular energy production, and their dysfunction can trigger a compensatory increase in glycolytic flux to sustain cellular ATP levels. Here, we studied the mechanism of this homeostatic phenomenon in C2C12 myoblasts. Acute (30 min) mitoenergetic dysfunction induced by the mitochondrial inhibitors piericidin A and antimycin A stimulated Glut1-mediated glucose uptake without altering Glut1 (also known as SLC2A1) mRNA or plasma membrane levels. The serine/threonine liver kinase B1 (LKB1; also known as STK11) and AMP-activated protein kinase (AMPK) played a central role in this stimulation. In contrast, ataxia-telangiectasia mutated (ATM; a potential AMPK kinase) and hydroethidium (HEt)-oxidizing reactive oxygen species (ROS; increased in piericidin-A- and antimycin-A-treated cells) appeared not to be involved in the stimulation of glucose uptake. Treatment with mitochondrial inhibitors increased NAD+ and NADH levels (associated with a lower NAD+:NADH ratio) but did not affect the level of Glut1 acetylation. Stimulation of glucose uptake was greatly reduced by chemical inhibition of Sirt2 or mTOR-RAPTOR. We propose that mitochondrial dysfunction triggers LKB1-mediated AMPK activation, which stimulates Sirt2 phosphorylation, leading to activation of mTOR-RAPTOR and Glut1-mediated glucose uptake.
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Affiliation(s)
- Dania C Liemburg-Apers
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands
| | - Jori A L Wagenaars
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands
| | - Jan A M Smeitink
- Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands
| | - Peter H G M Willems
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands
| | - Werner J H Koopman
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands .,Centre for Systems Biology and Bioenergetics, Radboud University and Radboud University Medical Center, 6500HB, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands
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26
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Song HY, Park SH, Kang HJ, Vassilopoulos A. Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates. J Vis Exp 2016:53563. [PMID: 26966987 DOI: 10.3791/53563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Acetylation has emerged as an important post-translational modification (PTM) regulating a plethora of cellular processes and functions. This is further supported by recent findings in high-resolution mass spectrometry based proteomics showing that many new proteins and sites within these proteins can be acetylated. However the identity of the enzymes regulating these proteins and sites is often unknown. Among these enzymes, sirtuins, which belong to the class III histone lysine deacetylases, have attracted great interest as enzymes regulating the acetylome under different physiological or pathophysiological conditions. Here we describe methods to link SIRT2, the cytoplasmic sirtuin, with its substrates including both in vitro and in vivo deacetylation assays. These assays can be applied in studies focused on other members of the sirtuin family to unravel the specific role of sirtuins and are necessary in order to establish the regulatory interplay of specific deacetylases with their substrates as a first step to better understand the role of protein acetylation. Furthermore, such assays can be used to distinguish functional acetylation sites on a protein from what may be non-regulatory acetylated lysines, as well as to examine the interplay between a deacetylase and its substrate in a physiological context.
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Affiliation(s)
- Ha Yong Song
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Seong-Hoon Park
- Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Hong-Jun Kang
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University
| | - Athanassios Vassilopoulos
- Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University;
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27
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LaBarge SA, Migdal CW, Buckner EH, Okuno H, Gertsman I, Stocks B, Barshop BA, Nalbandian SR, Philp A, McCurdy CE, Schenk S. p300 is not required for metabolic adaptation to endurance exercise training. FASEB J 2015; 30:1623-33. [PMID: 26712218 DOI: 10.1096/fj.15-281741] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/11/2015] [Indexed: 11/11/2022]
Abstract
The acetyltransferase, E1a-binding protein (p300), is proposed to regulate various aspects of skeletal muscle development, metabolism, and mitochondrial function,viaits interaction with numerous transcriptional regulators and other proteins. Remarkably, however, the contribution of p300 to skeletal muscle function and metabolism,in vivo, is poorly understood. To address this, we used Cre-LoxP methodology to generate mice with skeletal muscle-specific knockout of E1a-binding protein (mKO). mKO mice were indistinguishable from their wild-type/floxed littermates, with no differences in lean mass, skeletal muscle structure, fiber type, respirometry flux, or metabolites of fatty acid and amino acid metabolism.Ex vivomuscle function in extensor digitorum longus and soleus muscles, including peak stress and time to fatigue, as well asin vivorunning capacity were also comparable. Moreover, expected adaptations to a 20 d voluntary wheel running regime were not compromised in mKO mice. Taken together, these findings demonstrate that p300 is not required for the normal development or functioning of adult skeletal muscle, nor is it required for endurance exercise-mediated mitochondrial adaptations.-LaBarge, S. A., Migdal, C. W., Buckner, E. H., Okuno, H., Gertsman, I., Stocks, B., Barshop, B. A., Nalbandian, S. R., Philp, A., McCurdy, C. E., Schenk, S. p300 is not required for metabolic adaptation to endurance exercise training.
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Affiliation(s)
- Samuel A LaBarge
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Christopher W Migdal
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Elisa H Buckner
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Hiroshi Okuno
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Ilya Gertsman
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Ben Stocks
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Bruce A Barshop
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Sarah R Nalbandian
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Andrew Philp
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Carrie E McCurdy
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
| | - Simon Schenk
- *Department of Orthopaedic Surgery and Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA; School of Sport, Exercise, and Rehabilitation Sciences, University of Birmingham, Edgbaston, United Kingdom; and Department of Human Physiology, University of Oregon, Eugene, Oregon, USA
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28
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Abstract
Acute and transient changes in gene transcription following a single exercise bout, if reinforced by repeated exercise stimuli, result in the longer lasting effects on protein expression and function that form the basis of skeletal muscle training adaptations. Changes in skeletal muscle gene expression occur in response to multiple stimuli associated with skeletal muscle contraction, various signaling kinases that respond to these stimuli, and numerous downstream pathways and targets of these kinases. In addition, DNA methylation, histone acetylation and phosphorylation, and micro-RNAs can alter gene expression via epigenetic mechanisms. Contemporary studies rely upon "big omics data," in combination with computational and systems biology, to interrogate, and make sense of, the complex interactions underpinning exercise adaptations. The exciting potential is a greater understanding of the integrative biology of exercise.
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Affiliation(s)
- Mark Hargreaves
- Department of Physiology, The University of Melbourne, Melbourne, Australia.
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29
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Decroos C, Christianson DW. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry 2015. [PMID: 26200446 DOI: 10.1021/acs.biochem.5b00536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Polyamines are essential aliphatic polycations that bind to nucleic acids and accordingly are involved in a variety of cellular processes. Polyamine function can be regulated by acetylation and deacetylation, just as histone function can be regulated by lysine acetylation and deacetylation. Acetylpolyamine amidohydrolase (APAH) from Mycoplana ramosa is a zinc-dependent polyamine deacetylase that shares approximately 20% amino acid sequence identity with human histone deacetylases. We now report the X-ray crystal structures of APAH-inhibitor complexes in a new and superior crystal form that diffracts to very high resolution (1.1-1.4 Å). Inhibitors include previously synthesized analogues of N(8)-acetylspermidine bearing trifluoromethylketone, thiol, and hydroxamate zinc-binding groups [Decroos, C., Bowman, C. M., and Christianson, D. W. (2013) Bioorg. Med. Chem. 21, 4530], and newly synthesized hydroxamate analogues of shorter, monoacetylated diamines, the most potent of which is the hydroxamate analogue of N-acetylcadaverine (IC50 = 68 nM). The high-resolution crystal structures of APAH-inhibitor complexes provide key inferences about the inhibition and catalytic mechanism of zinc-dependent deacetylases. For example, the trifluoromethylketone analogue of N(8)-acetylspermidine binds as a tetrahedral gem-diol that mimics the tetrahedral intermediate and its flanking transition states in catalysis. Surprisingly, this compound is also a potent inhibitor of human histone deacetylase 8 with an IC50 of 260 nM. Crystal structures of APAH-inhibitor complexes are determined at the highest resolution of any currently existing zinc deacetylase structure and thus represent the most accurate reference points for understanding structure-mechanism and structure-inhibition relationships in this critically important enzyme family.
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Affiliation(s)
- Christophe Decroos
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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30
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Donnelly MR, Ciborowski P. Proteomics, biomarkers, and HIV-1: A current perspective. Proteomics Clin Appl 2015; 10:110-25. [PMID: 26033875 PMCID: PMC4666820 DOI: 10.1002/prca.201500002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 01/24/2023]
Abstract
Despite more than three decades of extensive research, HIV‐1 infection although well controlled with cART, remains incurable. Multifactorial complexity of the viral life‐cycle poses great challenges in understanding molecular mechanisms underlying this infection and the development of biomarkers, which we hope will lead us to its eradication. For a more in‐depth understanding of how the virus interacts with host target cells, T cells and macrophages, proteomic profiling techniques that offer strategies to investigate the proteome in its entirety were employed. Here, we review proteomic studies related to HIV‐1 infection and discuss perspectives and limitations of proteomic and systems biology approaches in future studies.
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Affiliation(s)
- Maire Rose Donnelly
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
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31
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LaBarge S, Migdal C, Schenk S. Is acetylation a metabolic rheostat that regulates skeletal muscle insulin action? Mol Cells 2015; 38:297-303. [PMID: 25824547 PMCID: PMC4400303 DOI: 10.14348/molcells.2015.0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 12/11/2022] Open
Abstract
Skeletal muscle insulin resistance, which increases the risk for developing various metabolic diseases, including type 2 diabetes, is a common metabolic disorder in obesity and aging. If potential treatments are to be developed to treat insulin resistance, then it is important to fully understand insulin signaling and glucose metabolism. While recent large-scale "omics" studies have revealed the acetylome to be comparable in size to the phosphorylome, the acetylation of insulin signaling proteins and its functional relevance to insulin-stimulated glucose transport and glucose metabolism is not fully understood. In this Mini Review we discuss the acetylation status of proteins involved in the insulin signaling pathway and review their potential effect on, and relevance to, insulin action in skeletal muscle.
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Affiliation(s)
- Samuel LaBarge
- Department of Orthopaedic Surgery, University of California, San Diego, CA, 92093,
USA
| | - Christopher Migdal
- Department of Orthopaedic Surgery, University of California, San Diego, CA, 92093,
USA
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, San Diego, CA, 92093,
USA
- Biomedical Sciences Graduate Program, University of California, San Diego, CA, 92093,
USA
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