351
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Liu X, Wei W, Liu Y, Yang X, Wu J, Zhang Y, Zhang Q, Shi T, Du JX, Zhao Y, Lei M, Zhou JQ, Li J, Wong J. MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300. Cell Discov 2017; 3:17016. [PMID: 28580166 PMCID: PMC5441097 DOI: 10.1038/celldisc.2017.16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022] Open
Abstract
Recent studies indicate that histones are subjected to various types of acylation including acetylation, propionylation and crotonylation. CBP and p300 have been shown to catalyze multiple types of acylation but are not conserved in evolution, raising the question as to the existence of other enzymes for histone acylation and the functional relationship between well-characterized acetylation and other types of acylation. In this study, we focus on enzymes catalyzing histone crotonylation and demonstrate that among the known histone acetyltransferases, MOF, in addition to CBP and p300, also possesses histone crotonyltransferase (HCT) activity and this activity is conserved in evolution. We provide evidence that CBP and p300 are the major HCTs in mammalian cells. Furthermore, we have generated novel CBP/p300 mutants with deficient histone acetyltransferase but competent HCT activity. These CBP/p300 mutants can substitute the endogenous CBP/p300 to enhance transcriptional activation in the cell, which correlates with enhanced promoter crotonylation and recruitment of DPF2, a selective reader for crotonylated histones. Taken together, we have identified MOF as an evolutionarily conserved HCT and provide first cellular evidence that CBP/p300 can facilitate transcriptional activation through histone acylation other than acetylation, thus supporting an emerging role for the non-acetylation type of histone acylation in transcription and possibly other chromatin-based processes.
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Affiliation(s)
- Xiaoguang Liu
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuting Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xueli Yang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian Wu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yang Zhang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Qiao Zhang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Ming Lei
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin-Qiu Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Joint Research Center for Translational Medicine, East China Normal University and Shanghai Fengxian District Central Hospital, Shanghai, China
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352
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Xu H, Zhou J, Lin S, Deng W, Zhang Y, Xue Y. PLMD: An updated data resource of protein lysine modifications. J Genet Genomics 2017; 44:243-250. [PMID: 28529077 DOI: 10.1016/j.jgg.2017.03.007] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/26/2017] [Accepted: 03/30/2017] [Indexed: 01/08/2023]
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353
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Nie L, Shuai L, Zhu M, Liu P, Xie ZF, Jiang S, Jiang HW, Li J, Zhao Y, Li JY, Tan M. The Landscape of Histone Modifications in a High-Fat Diet-Induced Obese (DIO) Mouse Model. Mol Cell Proteomics 2017; 16:1324-1334. [PMID: 28450421 DOI: 10.1074/mcp.m117.067553] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Indexed: 12/24/2022] Open
Abstract
Type 2 diabetes (T2D) is a major chronic healthcare concern worldwide. Emerging evidence suggests that a histone-modification-mediated epigenetic mechanism underlies T2D. Nevertheless, the dynamics of histone marks in T2D have not yet been carefully analyzed. Using a mass spectrometry-based label-free and chemical stable isotope labeling quantitative proteomic approach, we systematically profiled liver histone post-translational modifications (PTMs) in a prediabetic high-fat diet-induced obese (DIO) mouse model. We identified 170 histone marks, 30 of which were previously unknown. Interestingly, about 30% of the histone marks identified in DIO mouse liver belonged to a set of recently reported lysine acylation modifications, including propionylation, butyrylation, malonylation, and succinylation, suggesting possible roles of these newly identified histone acylations in diabetes and obesity. These histone marks were detected without prior affinity enrichment with an antibody, demonstrating that the histone acylation marks are present at reasonably high stoichiometry. Fifteen histone marks differed in abundance in DIO mouse liver compared with liver from chow-fed mice in label-free quantification, and six histone marks in stable isotope labeling quantification. Analysis of hepatic histone modifications from metformin-treated DIO mice revealed that metformin, a drug widely used for T2D, could reverse DIO-stimulated histone H3K36me2 in prediabetes, suggesting that this mark is likely associated with T2D development. Our study thus offers a comprehensive landscape of histone marks in a prediabetic mouse model, provides a resource for studying epigenetic functions of histone modifications in obesity and T2D, and suggest a new epigenetic mechanism for the physiological function of metformin.
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Affiliation(s)
- Litong Nie
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lin Shuai
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Mingrui Zhu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ping Liu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Zhi-Fu Xie
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shangwen Jiang
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Hao-Wen Jiang
- ‖College of Chemistry and Molecular Engineering, East China Normal University, China, 200062
| | - Jia Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Yingming Zhao
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,**Ben May Department for Cancer Research, University of Chicago, Chicago, IL
| | - Jing-Ya Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203;
| | - Minjia Tan
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203; .,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
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354
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Ren J, Sang Y, Lu J, Yao YF. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol 2017; 25:768-779. [PMID: 28462789 DOI: 10.1016/j.tim.2017.04.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
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Affiliation(s)
- Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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355
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The therapeutic hope for HDAC6 inhibitors in malignancy and chronic disease. Clin Sci (Lond) 2017; 130:987-1003. [PMID: 27154743 DOI: 10.1042/cs20160084] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 12/12/2022]
Abstract
Recent years have witnessed an emergence of a new class of therapeutic agents, termed histone deacetylase 6 (HDAC6) inhibitors. HDAC6 is one isoform of a family of HDAC enzymes that catalyse the removal of functional acetyl groups from proteins. It stands out from its cousins in almost exclusively deacetylating cytoplasmic proteins, in exerting deacetylation-independent effects and in the success that has been achieved in developing relatively isoform-specific inhibitors of its enzymatic action that have reached clinical trial. HDAC6 plays a pivotal role in the removal of misfolded proteins and it is this role that has been most successfully targeted to date. HDAC6 inhibitors are being investigated for use in combination with proteasome inhibitors for the treatment of lymphoid malignancies, whereby HDAC6-dependent protein disposal currently limits the cytotoxic effectiveness of the latter. Similarly, numerous recent studies have linked altered HDAC6 activity to the pathogenesis of neurodegenerative diseases that are characterized by misfolded protein accumulation. It seems likely though that the function of HDAC6 is not limited to malignancy and neurodegeneration, the deacetylase being implicated in a number of other cellular processes and diseases including in cardiovascular disease, inflammation, renal fibrosis and cystogenesis. Here, we review the unique features of HDAC6 that make it so appealing as a drug target and its currently understood role in health and disease. Whether HDAC6 inhibition will ultimately find a clinical niche in the treatment of malignancy or prevalent complex chronic diseases remains to be determined.
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356
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Trejo-Arellano MS, Mahrez W, Nakamura M, Moreno-Romero J, Nanni P, Köhler C, Hennig L. H3K23me1 is an evolutionarily conserved histone modification associated with CG DNA methylation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:293-303. [PMID: 28182313 DOI: 10.1111/tpj.13489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/09/2016] [Accepted: 01/16/2017] [Indexed: 05/14/2023]
Abstract
Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a histone modification not previously described in plants. H3K23me1 is an evolutionarily conserved mark in diverse species of flowering plants. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms. In transposable elements it co-localized with CG, CHG and CHH DNA methylation as well as with the heterochromatic histone mark H3K9me2. Transposable elements are often rich in H3K23me1 but different families vary in their enrichment: LTR-Gypsy elements are most enriched and RC/Helitron elements are least enriched. The histone methyltransferase KRYPTONITE and normal DNA methylation were required for normal levels of H3K23me1 on transposable elements. Immunostaining experiments confirmed the pericentromeric localization and also showed mild enrichment in less condensed regions. Accordingly, gene bodies of protein-coding genes had intermediate H3K23me1 levels, which coexisted with CG DNA methylation. Enrichment of H3K23me1 along gene bodies did not correlate with transcription levels. Together, this work establishes H3K23me1 as a so far undescribed component of the plant histone code.
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Affiliation(s)
- Minerva S Trejo-Arellano
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
| | - Walid Mahrez
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
- Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, Zurich, CH-8092, Switzerland
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
| | - Jordi Moreno-Romero
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, CH-8057, Switzerland
| | - Claudia Köhler
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden
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357
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Wei W, Mao A, Tang B, Zeng Q, Gao S, Liu X, Lu L, Li W, Du JX, Li J, Wong J, Liao L. Large-Scale Identification of Protein Crotonylation Reveals Its Role in Multiple Cellular Functions. J Proteome Res 2017; 16:1743-1752. [PMID: 28234478 DOI: 10.1021/acs.jproteome.7b00012] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lysine crotonylation on histones is a recently identified post-translational modification that has been demonstrated to associate with active promoters and to directly stimulate transcription. Given that crotonyl-CoA is essential for the acyl transfer reaction and it is a metabolic intermediate widely localized within the cell, we postulate that lysine crotonylation on nonhistone proteins could also widely exist. Using specific antibody enrichment followed by high-resolution mass spectrometry analysis, we identified hundreds of crotonylated proteins and lysine residues. Bioinformatics analysis reveals that crotonylated proteins are particularly enriched for nuclear proteins involved in RNA processing, nucleic acid metabolism, chromosome organization, and gene expression. Furthermore, we demonstrate that crotonylation regulates HDAC1 activity, expels HP1α from heterochromatin, and inhibits cell cycle progression through S-phase. Our data thus indicate that lysine crotonylation could occur in a large number of proteins and could have important regulatory roles in multiple nuclei-related cellular processes.
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Affiliation(s)
- Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Anqi Mao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Bin Tang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Qiufang Zeng
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Shennan Gao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Xiaoguang Liu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Lu Lu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Wenpeng Li
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China.,Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center , Guangzhou 510060, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University , Shanghai 200241, China
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358
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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol 2017; 24:231-242. [PMID: 28163016 DOI: 10.1016/j.chembiol.2017.01.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023]
Abstract
Non-enzymatic protein modification driven by thioester reactivity is thought to play a major role in the establishment of cellular lysine acylation. However, the specific protein targets of this process are largely unknown. Here we report an experimental strategy to investigate non-enzymatic acylation in cells. Specifically, we develop a chemoproteomic method that separates thioester reactivity from enzymatic utilization, allowing selective enrichment of non-enzymatic acylation targets. Applying this method to cancer cell lines identifies numerous candidate targets of non-enzymatic acylation, including several enzymes in lower glycolysis. Functional studies highlight malonyl-CoA as a reactive thioester metabolite that can modify and inhibit glycolytic enzyme activity. Finally, we show that synthetic thioesters can be used as novel reagents to probe non-enzymatic acylation in living cells. Our studies provide new insights into the targets and drivers of non-enzymatic acylation, and demonstrate the utility of reactivity-based methods to experimentally investigate this phenomenon in biology and disease.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew J Worth
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julie M Garlick
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Allison M Roberts
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Clementina Mesaros
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Ian A Blair
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute, 3020 Market Street, Philadelphia, PA 19104, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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359
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Pelletier N, Grégoire S, Yang XJ. Assays for Acetylation and Other Acylations of Lysine Residues. ACTA ACUST UNITED AC 2017; 87:14.11.1-14.11.18. [PMID: 28150880 DOI: 10.1002/cpps.26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Lysine acetylation refers to addition of an acetyl moiety to the epsilon-amino group of a lysine residue and is important for regulating protein functions in various organisms from bacteria to humans. This is a reversible and precisely controlled covalent modification that either serves as an on/off switch or participates in a codified manner with other post-translational modifications to regulate different cellular and developmental processes in normal and pathological states. This unit describes methods for in vitro and in vivo determination of lysine acetylation. Such methods can be easily extended for analysis of other acylations (such as propionylation, butyrylation, crotonylation, and succinylation) that are also present in histones and many other proteins. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nadine Pelletier
- Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Serge Grégoire
- Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Xiang-Jiao Yang
- Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, Quebec, Canada
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360
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Wang ZA, Kurra Y, Wang X, Zeng Y, Lee YJ, Sharma V, Lin H, Dai SY, Liu WR. A Versatile Approach for Site-Specific Lysine Acylation in Proteins. Angew Chem Int Ed Engl 2017; 56:1643-1647. [PMID: 28042700 PMCID: PMC5550319 DOI: 10.1002/anie.201611415] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/13/2016] [Indexed: 11/09/2022]
Abstract
Using amber suppression in coordination with a mutant pyrrolysyl-tRNA synthetase-tRNAPyl pair, azidonorleucine is genetically encoded in E. coli. Its genetic incorporation followed by traceless Staudinger ligation with a phosphinothioester allows the convenient synthesis of a protein with a site-specifically installed lysine acylation. By simply changing the phosphinothioester identity, any lysine acylation type could be introduced. Using this approach, we demonstrated that both lysine acetylation and lysine succinylation can be installed selectively in ubiquitin and synthesized histone H3 with succinylation at its K4 position (H3K4su). Using an H3K4su-H4 tetramer as a substrate, we further confirmed that Sirt5 is an active histone desuccinylase. Lysine succinylation is a recently identified post-translational modification. The reported technique makes it possible to explicate regulatory functions of this modification in proteins.
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Affiliation(s)
- Zhipeng A Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Xin Wang
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Texas State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Susie Y Dai
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Texas State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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361
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Galligan JJ, Kingsley PJ, Wauchope OR, Mitchener MM, Camarillo JM, Wepy JA, Harris PS, Fritz KS, Marnett LJ. Quantitative Analysis and Discovery of Lysine and Arginine Modifications. Anal Chem 2017; 89:1299-1306. [PMID: 27982582 PMCID: PMC5309163 DOI: 10.1021/acs.analchem.6b04105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Post-translational modifications (PTMs) affect protein function, localization, and stability, yet very little is known about the ratios of these modifications. Here, we describe a novel method to quantitate and assess the relative stoichiometry of Lys and Arg modifications (QuARKMod) in complex biological settings. We demonstrate the versatility of this platform in monitoring recombinant protein modification of peptide substrates, PTMs of individual histones, and the relative abundance of these PTMs as a function of subcellular location. Lastly, we describe a product ion scanning technique that offers the potential to discover unexpected and possibly novel Lys and Arg modifications. In summary, this approach yields accurate quantitation and discovery of protein PTMs in complex biological systems without the requirement of high mass accuracy instrumentation.
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Affiliation(s)
- James J. Galligan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Philip J. Kingsley
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Orrette R. Wauchope
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Michelle M. Mitchener
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jeannie M. Camarillo
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - James A. Wepy
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Peter S. Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Kristofer S. Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Lawrence J. Marnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
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362
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Fujisawa T, Filippakopoulos P. Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol 2017; 18:246-262. [PMID: 28053347 DOI: 10.1038/nrm.2016.143] [Citation(s) in RCA: 418] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein-protein interaction modules that are found in a wide range of proteins with diverse catalytic and scaffolding functions and are present in most tissues. BRDs selectively recognize and bind to acetylated Lys residues - particularly in histones - and thereby have important roles in the regulation of gene expression. BRD-containing proteins are frequently dysregulated in cancer, they participate in gene fusions that generate diverse, frequently oncogenic proteins, and many cancer-causing mutations have been mapped to the BRDs themselves. Importantly, BRDs can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
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Affiliation(s)
- Takao Fujisawa
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford.,Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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363
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Wang ZA, Kurra Y, Wang X, Zeng Y, Lee YJ, Sharma V, Lin H, Dai SY, Liu WR. A Versatile Approach for Site-Specific Lysine Acylation in Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Zhipeng A. Wang
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
| | - Yadagiri Kurra
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
| | - Xin Wang
- Department of Plant Pathology and Microbiology; Institute for Plant Genomics; Office of the Texas State Chemist; Department of Veterinary Pathobiology; College Station TX 77843 USA
| | - Yu Zeng
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
| | - Yan-Jiun Lee
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
| | - Vangmayee Sharma
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology; Cornell University; Ithaca NY 14853 USA
| | - Susie Y. Dai
- Department of Plant Pathology and Microbiology; Institute for Plant Genomics; Office of the Texas State Chemist; Department of Veterinary Pathobiology; College Station TX 77843 USA
| | - Wenshe R. Liu
- Department of Chemistry; Texas A&M University; College Station TX 77843 USA
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364
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Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28639249 DOI: 10.1007/5584_2017_58] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions. First, some "non-classical" histone modifications, such as short-chain acylations other than acetylation, are considered to conclude that their relationship with the concentration of metabolic intermediaries might make of them a sensor of the physiological state of the cells. Then attention is paid to the interest of studying chromatin organisation and epigenetic marks at a single nucleosome level as a complement to genome-wide approaches. Finally, as a consequence of the above questions, the review focuses on the presence of multiple histone post-translational modifications on a single nucleosome. The methods to detect them and their meaning, with special emphasis on bivalent marks, are discussed.
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365
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Wang HL, Liu S, Yu ZJ, Wu C, Cheng L, Wang Y, Chen K, Zhou S, Chen Q, Yu Y, Li GB. Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design. RSC Adv 2017. [DOI: 10.1039/c7ra05824a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biophysical and crystallographic analyses of small-molecule substrates with sirtuins provide thermodynamic insights and key pharmacophore features for inhibitor design.
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Affiliation(s)
- Hua-Li Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Sha Liu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Chengyong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Linna Cheng
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Yuxi Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Kai Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Shu Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Qiang Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Yamei Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
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366
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Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL. Quantitative Proteomics Reveals Fundamental Regulatory Differences in Oncogenic HRAS and Isocitrate Dehydrogenase (IDH1) Driven Astrocytoma. Mol Cell Proteomics 2017; 16:39-56. [PMID: 27834733 PMCID: PMC5217781 DOI: 10.1074/mcp.m116.063883] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/04/2016] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma multiformes (GBMs) are high-grade astrocytomas and the most common brain malignancies. Primary GBMs are often associated with disturbed RAS signaling, and expression of oncogenic HRAS results in a malignant phenotype in glioma cell lines. Secondary GBMs arise from lower-grade astrocytomas, have slower progression than primary tumors, and contain IDH1 mutations in over 70% of cases. Despite significant amount of accumulating genomic and transcriptomic data, the fundamental mechanistic differences of gliomagenesis in these two types of high-grade astrocytoma remain poorly understood. Only a few studies have attempted to investigate the proteome, phosphorylation signaling, and epigenetic regulation in astrocytoma. In the present study, we applied quantitative phosphoproteomics to identify the main signaling differences between oncogenic HRAS and mutant IDH1-driven glioma cells as models of primary and secondary GBM, respectively. Our analysis confirms the driving roles of the MAPK and PI3K/mTOR signaling pathways in HRAS driven cells and additionally uncovers dysregulation of other signaling pathways. Although a subset of the signaling changes mediated by HRAS could be reversed by a MEK inhibitor, dual inhibition of MEK and PI3K resulted in more complete reversal of the phosphorylation patterns produced by HRAS expression. In contrast, cells expressing mutant IDH1 did not show significant activation of MAPK or PI3K/mTOR pathways. Instead, global downregulation of protein expression was observed. Targeted proteomic analysis of histone modifications identified significant histone methylation, acetylation, and butyrylation changes in the mutant IDH1 expressing cells, consistent with a global transcriptional repressive state. Our findings offer novel mechanistic insight linking mutant IDH1 associated inhibition of histone demethylases with specific histone modification changes to produce global transcriptional repression in secondary glioblastoma. Our proteomic datasets are available for download and provide a comprehensive catalogue of alterations in protein abundance, phosphorylation, and histone modifications in oncogenic HRAS and IDH1 driven astrocytoma cells beyond the transcriptomic level.
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Affiliation(s)
- Sophia Doll
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - Anatoly Urisman
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - Juan A Oses-Prieto
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California
| | - David Arnott
- §Department of Protein Chemistry, Genentech Inc, South San Francisco, 94158-2517 California
| | - Alma L Burlingame
- From the ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158-2517 California;
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367
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YOSHIDA M, KUDO N, KOSONO S, ITO A. Chemical and structural biology of protein lysine deacetylases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:297-321. [PMID: 28496053 PMCID: PMC5489435 DOI: 10.2183/pjab.93.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/21/2017] [Indexed: 05/27/2023]
Abstract
Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD+-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer. Notably, drug discovery efforts have achieved success in developing HDAC-targeting therapeutics for treatment of several cancers. However, recent advancements in proteomics technology have revealed much broader aspects of HDACs beyond gene expression control. Not only histones but also a large number of cellular proteins are subject to acetylation by histone acetyltransferases (HATs) and deacetylation by HDACs. Furthermore, some of their structures can flexibly accept and hydrolyze other acyl groups on protein lysine residues. This review mainly focuses on structural aspects of HDAC enzymatic activity regulated by interaction with substrates, co-factors, small molecule inhibitors, and activators.
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Affiliation(s)
- Minoru YOSHIDA
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Norio KUDO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Saori KOSONO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Akihiro ITO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
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368
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Abstract
Bioactive electrophiles generated from the oxidation of endogenous and exogenous compounds are a contributing factor in numerous disease states. Their toxicity is largely attributed to the covalent modification of cellular nucleophiles, including protein and DNA. With regard to protein modification, the side-chains of Cys, His, Lys, and Arg residues are critical targets. This results in the generation of undesired protein post-translational modifications (PTMs) that can trigger dire cellular consequences. Notably, histones are Lys- and Arg-rich proteins, providing a fertile source for adduction by both exogenous and endogenous electrophiles. The regulation of histone PTMs plays a critical role in the regulation of chromatin structure and thus gene expression. This perspective focuses on the role of electrophilic protein adduction within the context of chromatin and its potential consequences on cellular law and order.
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Affiliation(s)
- James J Galligan
- Department of Biochemistry, ‡Department of Chemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Lawrence J Marnett
- Department of Biochemistry, ‡Department of Chemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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369
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A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome. Proc Natl Acad Sci U S A 2016; 114:125-130. [PMID: 27999180 DOI: 10.1073/pnas.1611431114] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kabuki syndrome is a Mendelian intellectual disability syndrome caused by mutations in either of two genes (KMT2D and KDM6A) involved in chromatin accessibility. We previously showed that an agent that promotes chromatin opening, the histone deacetylase inhibitor (HDACi) AR-42, ameliorates the deficiency of adult neurogenesis in the granule cell layer of the dentate gyrus and rescues hippocampal memory defects in a mouse model of Kabuki syndrome (Kmt2d+/βGeo). Unlike a drug, a dietary intervention could be quickly transitioned to the clinic. Therefore, we have explored whether treatment with a ketogenic diet could lead to a similar rescue through increased amounts of beta-hydroxybutyrate, an endogenous HDACi. Here, we report that a ketogenic diet in Kmt2d+/βGeo mice modulates H3ac and H3K4me3 in the granule cell layer, with concomitant rescue of both the neurogenesis defect and hippocampal memory abnormalities seen in Kmt2d+/βGeo mice; similar effects on neurogenesis were observed on exogenous administration of beta-hydroxybutyrate. These data suggest that dietary modulation of epigenetic modifications through elevation of beta-hydroxybutyrate may provide a feasible strategy to treat the intellectual disability seen in Kabuki syndrome and related disorders.
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370
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Kim MS, Zhong J, Pandey A. Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics 2016; 16:700-14. [PMID: 26667783 DOI: 10.1002/pmic.201500355] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/05/2015] [Accepted: 12/08/2015] [Indexed: 12/29/2022]
Abstract
Mass spectrometry (MS) is a powerful tool to analyze complex mixtures of proteins in a high-throughput fashion. Proteome analysis has already become a routine task in biomedical research with the emergence of proteomics core facilities in most research institutions. Post-translational modifications (PTMs) represent a mechanism by which complex biological processes are orchestrated dynamically at the systems level. MS is rapidly becoming popular to discover new modifications and novel sites of known PTMs, revolutionizing the current understanding of diverse signaling pathways and biological processes. However, MS-based analysis of PTMs has its own caveats and pitfalls that can lead to erroneous conclusions. Here, we review the most common errors in MS-based PTM analyses with the goal of adopting strategies that maximize correct interpretation in the context of biological questions that are being addressed. Finally, we provide suggestions that should help mass spectrometrists, bioinformaticians and biologists to perform and interpret MS-based PTM analyses more accurately.
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Affiliation(s)
- Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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371
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Proteome-wide identification of lysine propionylation in thermophilic and mesophilic bacteria: Geobacillus kaustophilus, Thermus thermophilus, Escherichia coli, Bacillus subtilis, and Rhodothermus marinus. Extremophiles 2016; 21:283-296. [DOI: 10.1007/s00792-016-0901-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/27/2016] [Indexed: 12/22/2022]
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372
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Metabolic regulation of gene expression through histone acylations. Nat Rev Mol Cell Biol 2016; 18:90-101. [PMID: 27924077 DOI: 10.1038/nrm.2016.140] [Citation(s) in RCA: 736] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Eight types of short-chain Lys acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggests that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this Review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, the acylation 'reader' proteins that mediate the effects of different acylations and their physiological functions, which include signal-dependent gene activation, spermatogenesis, tissue injury and metabolic stress. We propose a model to explain our present understanding of how differential histone acylation is regulated by the metabolism of the different acyl-CoA forms, which in turn modulates the regulation of gene expression.
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373
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Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
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Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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374
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Okanishi H, Kim K, Fukui K, Yano T, Kuramitsu S, Masui R. Proteome-wide identification of lysine succinylation in thermophilic and mesophilic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:232-242. [PMID: 27888076 DOI: 10.1016/j.bbapap.2016.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/13/2016] [Accepted: 11/19/2016] [Indexed: 02/07/2023]
Abstract
Lysine succinylation, one of post-translational acylations conserved from eukaryotes to bacteria, plays regulatory roles in various cellular processes. However, much remains unknown about the general and specific characteristics of lysine succinylation among bacteria, and about its functions different from those of other acylations. In this study, we characterized lysine succinylation, a newly discovered widespread type of lysine acylation in five bacterial species with different characteristics such as optimal growth temperature and cell wall structure. This study is the first to demonstrate that succinylation is general phenomenon occurring not only in mesophiles but also in thermophiles. Mapping of succinylation sites on protein structures revealed that succinylation occurs at many lysine residues important for protein function. Comparison of the succinylation sites in the five bacterial species provides insights regarding common protein regulation mechanisms utilizing lysine succinylation. Many succinylation sites were conserved among five bacteria, especially between Geobacillus kaustophilus and Bacillus subtilis, some of which are functionally important sites. Furthermore, systematic comparison of the succinyl-proteome results and our previous propionyl-proteome results showed that the abundance of these two types of acylations is considerably different among the five bacteria investigated. Many succinylation and propionylation events were detected in G. kaustophilus, whereas Escherichia coli and B. subtilis exhibited high succinylation and low propionylation; low succinylation and high propionylation were identified in Thermus thermophilus, and low succinylation and propionylation were observed in Rhodothermus marinus. Comparison of the characteristics of lysine succinylation and lysine propionylation suggested these two types of acylation play different roles in cellular processes.
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Affiliation(s)
- Hiroki Okanishi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; Division of Biology & Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Kwang Kim
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| | - Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; Division of Biology & Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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375
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Sun M, Xu J, Wu Z, Zhai L, Liu C, Cheng Z, Xu G, Tao S, Ye BC, Zhao Y, Tan M. Characterization of Protein Lysine Propionylation in Escherichia coli: Global Profiling, Dynamic Change, and Enzymatic Regulation. J Proteome Res 2016; 15:4696-4708. [DOI: 10.1021/acs.jproteome.6b00798] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mingwei Sun
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Junyu Xu
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- Lab
of Biosystems and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Zhixiang Wu
- Pediatric
Surgery Department, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, P. R. China
| | - Linhui Zhai
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chengxi Liu
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, P. R. China
| | - Guofeng Xu
- Pediatric
Surgery Department, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, P. R. China
| | - Shengce Tao
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Bang-Ce Ye
- Lab
of Biosystems and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yingming Zhao
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- Ben
May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, United States
| | - Minjia Tan
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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376
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Kaczmarska Z, Ortega E, Goudarzi A, Huang H, Kim S, Márquez JA, Zhao Y, Khochbin S, Panne D. Structure of p300 in complex with acyl-CoA variants. Nat Chem Biol 2016; 13:21-29. [PMID: 27820805 DOI: 10.1038/nchembio.2217] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/14/2016] [Indexed: 12/29/2022]
Abstract
Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer. Lysine substrate binding is predicted to remodel the acyl-CoA ligands into a conformation compatible with acyl-chain transfer. This remodeling requires that the aliphatic portion of acyl-CoA be accommodated in a hydrophobic pocket in the enzymes active site. The size of the pocket and its aliphatic nature exclude long-chain and charged acyl-CoA variants, presumably explaining the cofactor preference for p300.
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Affiliation(s)
| | - Esther Ortega
- European Molecular Biology Laboratory, Grenoble, France
| | - Afsaneh Goudarzi
- Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | - He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA
| | - Sunjoo Kim
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA
| | | | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA
| | - Saadi Khochbin
- Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France
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377
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Hirsch CL, Wrana JL, Dent SYR. KATapulting toward Pluripotency and Cancer. J Mol Biol 2016; 429:1958-1977. [PMID: 27720985 DOI: 10.1016/j.jmb.2016.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/30/2016] [Indexed: 12/20/2022]
Abstract
Development is generally regarded as a unidirectional process that results in the acquisition of specialized cell fates. During this process, cellular identity is precisely defined by signaling cues that tailor the chromatin landscape for cell-specific gene expression programs. Once established, these pathways and cell states are typically resistant to disruption. However, loss of cell identity occurs during tumor initiation and upon injury response. Moreover, terminally differentiated cells can be experimentally provoked to become pluripotent. Chromatin reorganization is key to the establishment of new gene expression signatures and thus new cell identity. Here, we explore an emerging concept that lysine acetyltransferase (KAT) enzymes drive cellular plasticity in the context of somatic cell reprogramming and tumorigenesis.
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Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada.
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
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378
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Kim SY, Sim CK, Zhang Q, Tang H, Brunmeir R, Pan H, Karnani N, Han W, Zhang K, Xu F. An Alternative Strategy for Pan-acetyl-lysine Antibody Generation. PLoS One 2016; 11:e0162528. [PMID: 27606599 PMCID: PMC5015836 DOI: 10.1371/journal.pone.0162528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023] Open
Abstract
Lysine acetylation is an important post-translational modification in cell signaling. In acetylome studies, a high-quality pan-acetyl-lysine antibody is key to successful enrichment of acetylated peptides for subsequent mass spectrometry analysis. Here we show an alternative method to generate polyclonal pan-acetyl-lysine antibodies using a synthesized random library of acetylated peptides as the antigen. Our antibodies are tested to be specific for acetyl-lysine peptides/proteins via ELISA and dot blot. When pooled, five of our antibodies show broad reactivity to acetyl-lysine peptides, complementing a commercial antibody in terms of peptide coverage. The consensus sequence of peptides bound by our antibody cocktail differs slightly from that of the commercial antibody. Lastly, our antibodies are tested in a proof-of-concept to analyze the acetylome of HEK293 cells. In total we identified 1557 acetylated peptides from 416 proteins. We thus demonstrated that our antibodies are well-qualified for acetylome studies and can complement existing commercial antibodies.
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Affiliation(s)
- Sun-Yee Kim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Choon Kiat Sim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Qiongyi Zhang
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Hui Tang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Reinhard Brunmeir
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Hong Pan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Weiping Han
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail: (KZ); (FX)
| | - Feng Xu
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
- * E-mail: (KZ); (FX)
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379
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Zhdanov R, Schirmer E, Venkatasubramani AV, Kerr A, Mandrou E, Rodriguez Blanco G, Kagansky A. Lipids contribute to epigenetic control via chromatin structure and functions. SCIENCEOPEN RESEARCH 2016. [DOI: 10.14293/s2199-1006.1.sor-life.auxytr.v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Isolated cases of experimental evidence over the last few decades have shown that, where specifically tested, both prokaryotes and eukaryotes have specific lipid species bound to nucleoproteins of the genome. In vitro, some of these lipid species exhibit stoichiometric association with DNA polynucleotides with differential affinities toward certain secondary and tertiary structures. Hydrophobic interactions with inner nuclear membrane could provide attractive anchor points for lipid-modified nucleoproteins in organizing the dynamic genome and accordingly there are precedents for covalent bonds between lipids and core histones and, under certain conditions, even DNA. Advances in biophysics, functional genomics, and proteomics in recent years brought about the first sparks of light that promises to uncover some coherent new level of the epigenetic code governed by certain types of lipid–lipid, DNA–lipid, and DNA-protein–lipid interactions among other biochemical lipid transactions in the nucleus. Here, we review some of the older and more recent findings and speculate on how critical nuclear lipid transactions are for individual cells, tissues, and organisms.
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380
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Li L, Shi L, Yang S, Yan R, Zhang D, Yang J, He L, Li W, Yi X, Sun L, Liang J, Cheng Z, Shi L, Shang Y, Yu W. SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability. Nat Commun 2016; 7:12235. [PMID: 27436229 PMCID: PMC4961794 DOI: 10.1038/ncomms12235] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/14/2016] [Indexed: 01/03/2023] Open
Abstract
Although SIRT7 is a member of sirtuin family proteins that are described as NAD+-dependent class III histone deacetylases, the intrinsic enzymatic activity of this sirtuin protein remains to be investigated and the cellular function of SIRT7 remains to be explored. Here we report that SIRT7 is an NAD+-dependent histone desuccinylase. We show that SIRT7 is recruited to DNA double-strand breaks (DSBs) in a PARP1-dependent manner and catalyses desuccinylation of H3K122 therein, thereby promoting chromatin condensation and DSB repair. We demonstrate that depletion of SIRT7 impairs chromatin compaction during DNA-damage response and sensitizes cells to genotoxic stresses. Our study indicates SIRT7 is a histone desuccinylase, providing a molecular basis for the understanding of epigenetic regulation by this sirtuin protein. Our experiments reveal that SIRT7-catalysed H3K122 desuccinylation is critically implemented in DNA-damage response and cell survival, providing a mechanistic insight into the cellular function of SIRT7. SIRT7 is a member of sirtuin family proteins that are described as NAD+-dependent class III histone deacetylases. Here, the authors show that SIRT7 is histone desuccinylase catalysing H3K122 desuccinylation, thereby promoting chromatin condensation and repair of DNA double strand breaks.
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Affiliation(s)
- Lei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lan Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shangda Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Ruorong Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Di Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou 310018, China
| | - Lei Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wenhua Yu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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381
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Cohen TJ, Constance BH, Hwang AW, James M, Yuan CX. Intrinsic Tau Acetylation Is Coupled to Auto-Proteolytic Tau Fragmentation. PLoS One 2016; 11:e0158470. [PMID: 27383765 PMCID: PMC4934699 DOI: 10.1371/journal.pone.0158470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/16/2016] [Indexed: 11/18/2022] Open
Abstract
Tau proteins are abnormally aggregated in a range of neurodegenerative tauopathies including Alzheimer’s disease (AD). Recently, tau has emerged as an extensively post-translationally modified protein, among which lysine acetylation is critical for normal tau function and its pathological aggregation. Here, we demonstrate that tau isoforms have different propensities to undergo lysine acetylation, with auto-acetylation occurring more prominently within the lysine-rich microtubule-binding repeats. Unexpectedly, we identified a unique intrinsic property of tau in which auto-acetylation induces proteolytic tau cleavage, thereby generating distinct N- and C-terminal tau fragments. Supporting a catalytic reaction-based mechanism, mapping and mutagenesis studies showed that tau cysteines, which are required for acetyl group transfer, are also essential for auto-proteolytic tau processing. Further mass spectrometry analysis identified the C-terminal 2nd and 4th microtubule binding repeats as potential sites of auto-cleavage. The identification of acetylation-mediated auto-proteolysis provides a new biochemical mechanism for tau self-regulation and warrants further investigation into whether auto-catalytic functions of tau are implicated in AD and other tauopathies.
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Affiliation(s)
- Todd J. Cohen
- Department of Neurology, UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Brian H. Constance
- Department of Neurology, UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Andrew W. Hwang
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael James
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chao-Xing Yuan
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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382
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Ringel AE, Wolberger C. Structural basis for acyl-group discrimination by human Gcn5L2. Acta Crystallogr D Struct Biol 2016; 72:841-8. [PMID: 27377381 PMCID: PMC4932917 DOI: 10.1107/s2059798316007907] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 11/10/2022] Open
Abstract
Gcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modifications in vivo, the acyl-chain specificity of the acetyltransferase human Gcn5 (Gcn5L2) was examined. Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 becomes progressively weaker with increasing acyl-chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA were determined. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor of Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl-chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group.
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Affiliation(s)
- Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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383
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Bleeker JC, Houtkooper RH. Sirtuin activation as a therapeutic approach against inborn errors of metabolism. J Inherit Metab Dis 2016; 39:565-72. [PMID: 27146436 PMCID: PMC4920849 DOI: 10.1007/s10545-016-9939-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/02/2023]
Abstract
Protein acylation has emerged as a large family of post translational modifications in which an acyl group can alter the function of a wide variety of proteins, especially in response to metabolic stress. The acylation state is regulated through reversible acylation/deacylation. Acylation occurs enzymatically or non-enzymatically, and responds to acyl-CoA levels. Deacylation on the other hand is controlled through the NAD(+)-dependent sirtuin proteins. In several inborn errors of metabolism (IEMs), accumulation of acyl-CoAs, due to defects in amino acid and fatty acid metabolic pathways, can lead to hyperacylation of proteins. This can have a direct effect on protein function and might play a role in pathophysiology. In this review we describe several mouse and cell models for IEM that display high levels of lysine acylation. Furthermore, we discuss how sirtuins serve as a promising therapeutic target to restore acylation state and could treat IEMs. In this context we examine several pharmacological sirtuin activators, such as resveratrol, NAD(+) precursors and PARP and CD38 inhibitors.
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Affiliation(s)
- Jeannette C Bleeker
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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384
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Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry. Curr Opin Chem Biol 2016; 33:142-50. [PMID: 27371874 DOI: 10.1016/j.cbpa.2016.06.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/13/2016] [Accepted: 06/08/2016] [Indexed: 01/01/2023]
Abstract
Histones are a group of proteins with a high number of post-translational modifications, including methylation, acetylation, phosphorylation, and monoubiquitination, which play critical roles in every chromatin-templated activity. The quantitative analysis of these modifications using mass spectrometry (MS) has seen significant improvements over the last decade. It is now possible to perform large-scale surveys of dozens of histone marks and hundreds of their combinations on global chromatin. Here, we review the development of three MS strategies for analyzing histone modifications that have come to be known as Bottom Up, Middle Down, and Top Down. We also discuss challenges and innovative solutions for characterizing and quantifying complicated isobaric species arising from multiple modifications on the same histone molecule.
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385
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Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics 2016; 12:499-517. [PMID: 26400466 DOI: 10.1586/14789450.2015.1084231] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.
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Affiliation(s)
- Özlem Önder
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA.,b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Carroll
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA
| | - Benjamin A Garcia
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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386
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 570] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
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387
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Resh MD. Fatty acylation of proteins: The long and the short of it. Prog Lipid Res 2016; 63:120-31. [PMID: 27233110 DOI: 10.1016/j.plipres.2016.05.002] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/19/2016] [Accepted: 05/21/2016] [Indexed: 12/22/2022]
Abstract
Long, short and medium chain fatty acids are covalently attached to hundreds of proteins. Each fatty acid confers distinct biochemical properties, enabling fatty acylation to regulate intracellular trafficking, subcellular localization, protein-protein and protein-lipid interactions. Myristate and palmitate represent the most common fatty acid modifying groups. New insights into how fatty acylation reactions are catalyzed, and how fatty acylation regulates protein structure and function continue to emerge. Myristate is typically linked to an N-terminal glycine, but recent studies reveal that lysines can also be myristoylated. Enzymes that remove N-terminal myristoyl-glycine or myristate from lysines have now been identified. DHHC proteins catalyze S-palmitoylation, but the mechanisms that regulate substrate recognition by individual DHHC family members remain to be determined. New studies continue to reveal thioesterases that remove palmitate from S-acylated proteins. Another area of rapid expansion is fatty acylation of the secreted proteins hedgehog, Wnt and Ghrelin, by Hhat, Porcupine and GOAT, respectively. Understanding how these membrane bound O-acyl transferases recognize their protein and fatty acyl CoA substrates is an active area of investigation, and is punctuated by the finding that these enzymes are potential drug targets in human diseases.
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Affiliation(s)
- Marilyn D Resh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 143, New York, NY 10075, United States.
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388
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Qian L, Nie L, Chen M, Liu P, Zhu J, Zhai L, Tao SC, Cheng Z, Zhao Y, Tan M. Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism. J Proteome Res 2016; 15:2060-71. [DOI: 10.1021/acs.jproteome.6b00264] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lili Qian
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Litong Nie
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ming Chen
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ping Liu
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, PR China
| | - Linhui Zhai
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Sheng-ce Tao
- Shanghai
Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, PR China
| | - Yingming Zhao
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Ben
May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, United States
| | - Minjia Tan
- The
Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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389
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Minshull TC, Cole J, Dockrell DH, Read RC, Dickman MJ. Analysis of histone post translational modifications in primary monocyte derived macrophages using reverse phase×reverse phase chromatography in conjunction with porous graphitic carbon stationary phase. J Chromatogr A 2016; 1453:43-53. [PMID: 27260198 PMCID: PMC4906248 DOI: 10.1016/j.chroma.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023]
Abstract
A two dimensional-liquid chromatography (2D-LC) based approach was developed for the identification and quantification of histone post translational modifications in conjunction with mass spectrometry analysis. Using a bottom-up strategy, offline 2D-LC was developed using reverse phase chromatography. A porous graphitic carbon stationary phase in the first dimension and a C18 stationary phase in the second dimension interfaced with mass spectrometry was used to analyse global levels of histone post translational modifications in human primary monocyte-derived macrophages. The results demonstrated that 84 different histone peptide proteoforms, with modifications at 18 different sites including combinatorial marks were identified, representing an increase in the identification of histone peptides by 65% and 51% compared to two different 1D-LC approaches on the same mass spectrometer. The use of the porous graphitic stationary phase in the first dimension resulted in efficient separation of histone peptides across the gradient, with good resolution and is orthogonal to the online C18 reverse phase chromatography. Overall, more histone peptides were identified using the 2D-LC approach compared to conventional 1D-LC approaches. In addition, a bioinformatic pipeline was developed in-house to enable the high throughput efficient and accurate quantification of fractionated histone peptides. The automation of a section of the downstream analysis pipeline increased the throughput of the 2D-LC-MS/MS approach for the quantification of histone post translational modifications.
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Affiliation(s)
- Thomas C Minshull
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom; Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - Joby Cole
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom; Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - David H Dockrell
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - Robert C Read
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine and Institute for Life Sciences, University of Southampton, NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton SO166YD, United Kingdom
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom.
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390
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SUMOylation Regulates Growth Factor Independence 1 in Transcriptional Control and Hematopoiesis. Mol Cell Biol 2016; 36:1438-50. [PMID: 26951200 DOI: 10.1128/mcb.01001-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/20/2016] [Indexed: 01/08/2023] Open
Abstract
Cell fate specification requires precise coordination of transcription factors and their regulators to achieve fidelity and flexibility in lineage allocation. The transcriptional repressor growth factor independence 1 (GFI1) is comprised of conserved Snail/Slug/Gfi1 (SNAG) and zinc finger motifs separated by a linker region poorly conserved with GFI1B, its closest homolog. Moreover, GFI1 and GFI1B coordinate distinct developmental fates in hematopoiesis, suggesting that their functional differences may derive from structures within their linkers. We show a binding interface between the GFI1 linker and the SP-RING domain of PIAS3, an E3-SUMO (small ubiquitin-related modifier) ligase. The PIAS3 binding region in GFI1 contains a conserved type I SUMOylation consensus element, centered on lysine-239 (K239). In silico prediction algorithms identify K239 as the only high-probability site for SUMO modification. We show that GFI1 is modified by SUMO at K239. SUMOylation-resistant derivatives of GFI1 fail to complement Gfi1 depletion phenotypes in zebrafish primitive erythropoiesis and granulocytic differentiation in cultured human cells. LSD1/CoREST recruitment and MYC repression by GFI1 are profoundly impaired for SUMOylation-resistant GFI1 derivatives, while enforced expression of MYC blocks granulocytic differentiation. These findings suggest that SUMOylation within the GFI1 linker favors LSD1/CoREST recruitment and MYC repression to govern hematopoietic differentiation.
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391
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Zhao D, Guan H, Zhao S, Mi W, Wen H, Li Y, Zhao Y, Allis CD, Shi X, Li H. YEATS2 is a selective histone crotonylation reader. Cell Res 2016; 26:629-32. [PMID: 27103431 PMCID: PMC4856769 DOI: 10.1038/cr.2016.49] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Dan Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Haipeng Guan
- MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shuai Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenyi Mi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genes and Development and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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392
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George J, Ahmad N. Mitochondrial Sirtuins in Cancer: Emerging Roles and Therapeutic Potential. Cancer Res 2016; 76:2500-6. [PMID: 27197261 DOI: 10.1158/0008-5472.can-15-2733] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/17/2016] [Indexed: 01/22/2023]
Abstract
The past few decades have witnessed a furious attention of scientific community toward identifying novel molecular factors and targets that could be exploited for drug development for cancer management. One such factor is the sirtuin (SIRT) family of nicotinamide adenine dinucleotide (NAD(+))-dependent deacetylases. The role of SIRTs in cancer is extremely complex, with dichotomous functions depending on cell contexts. Mammalian SIRTs (SIRT1-7) differ in their cellular localization and biologic functions. Among these, SIRT -3, -4, and -5 are located in the mitochondria and are being carefully investigated. These mitochondrial SIRTs (mtSIRT) regulate multiple cellular and physiologic processes, including cell cycle, gene expression, cell viability, stress response, metabolism, and energy homeostasis. Recent research suggests that mtSIRTs influence tumors by regulating the metabolic state of the cell. Although the research on the role of mtSIRTs in cancer is still in its infancy, studies have suggested tumor suppressor as well as tumor promoter roles for them. This review is focused on discussing up-to-date information about the roles and functional relevance of mtSIRTs (SIRT -3, -4, -5) in cancers. We have also provided a critical discussion and our perspective on their dual roles, as tumor promoter versus tumor suppressor, in cancer. Cancer Res; 76(9); 2500-6. ©2016 AACR.
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Affiliation(s)
- Jasmine George
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin. William S. Middleton VA Medical Center, Madison, Wisconsin.
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393
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Abstract
Sirtuins are NAD(+)-dependent enzymes universally present in all organisms, where they play central roles in regulating numerous biological processes. Although early studies showed that sirtuins deacetylated lysines in a reaction that consumes NAD(+), more recent studies have revealed that these enzymes can remove a variety of acyl-lysine modifications. The specificities for varied acyl modifications may thus underlie the distinct roles of the different sirtuins within a given organism. This review summarizes the structure, chemistry, and substrate specificity of sirtuins with a focus on how different sirtuins recognize distinct substrates and thus carry out specific functions.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185;
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14850;
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394
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Zhou L, Wang F, Sun R, Chen X, Zhang M, Xu Q, Wang Y, Wang S, Xiong Y, Guan KL, Yang P, Yu H, Ye D. SIRT5 promotes IDH2 desuccinylation and G6PD deglutarylation to enhance cellular antioxidant defense. EMBO Rep 2016; 17:811-22. [PMID: 27113762 DOI: 10.15252/embr.201541643] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 03/08/2016] [Indexed: 11/09/2022] Open
Abstract
Excess in mitochondrial reactive oxygen species (ROS) is considered as a major cause of cellular oxidative stress. NADPH, the main intracellular reductant, has a key role in keeping glutathione in its reduced form GSH, which scavenges ROS and thus protects the cell from oxidative damage. Here, we report that SIRT5 desuccinylates and deglutarylates isocitrate dehydrogenase 2 (IDH2) and glucose-6-phosphate dehydrogenase (G6PD), respectively, and thus activates both NADPH-producing enzymes. Moreover, we show that knockdown or knockout of SIRT5 leads to high levels of cellular ROS SIRT5 inactivation leads to the inhibition of IDH2 and G6PD, thereby decreasing NADPH production, lowering GSH, impairing the ability to scavenge ROS, and increasing cellular susceptibility to oxidative stress. Our study uncovers a SIRT5-dependent mechanism that regulates cellular NADPH homeostasis and redox potential by promoting IDH2 desuccinylation and G6PD deglutarylation.
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Affiliation(s)
- Lisha Zhou
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Renqiang Sun
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiufei Chen
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mengli Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Xu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shiwen Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Xiong
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kun-Liang Guan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Pengyuan Yang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongxiu Yu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dan Ye
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Shanghai, China Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
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395
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Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function. Proc Natl Acad Sci U S A 2016; 113:4320-5. [PMID: 27051063 DOI: 10.1073/pnas.1519858113] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellular metabolites, such as acyl-CoA, can modify proteins, leading to protein posttranslational modifications (PTMs). One such PTM is lysine succinylation, which is regulated by sirtuin 5 (SIRT5). Although numerous proteins are modified by lysine succinylation, the physiological significance of lysine succinylation and SIRT5 remains elusive. Here, by profiling acyl-CoA molecules in various mouse tissues, we have discovered that different tissues have different acyl-CoA profiles and that succinyl-CoA is the most abundant acyl-CoA molecule in the heart. This interesting observation has prompted us to examine protein lysine succinylation in different mouse tissues in the presence and absence of SIRT5. Protein lysine succinylation predominantly accumulates in the heart whenSirt5is deleted. Using proteomic studies, we have identified many cardiac proteins regulated by SIRT5. Our data suggest that ECHA, a protein involved in fatty acid oxidation, is a major enzyme that is regulated by SIRT5 and affects heart function.Sirt5knockout (KO) mice have lower ECHA activity, increased long-chain acyl-CoAs, and decreased ATP in the heart under fasting conditions.Sirt5KO mice develop hypertrophic cardiomyopathy, as evident from the increased heart weight relative to body weight, as well as reduced shortening and ejection fractions. These findings establish that regulating heart metabolism and function is a major physiological function of lysine succinylation and SIRT5.
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396
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Abstract
Histone posttranslational modifications represent a versatile set of epigenetic marks involved not only in dynamic cellular processes, such as transcription and DNA repair, but also in the stable maintenance of repressive chromatin. In this article, we review many of the key and newly identified histone modifications known to be deregulated in cancer and how this impacts function. The latter part of the article addresses the challenges and current status of the epigenetic drug development process as it applies to cancer therapeutics.
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Affiliation(s)
- James E Audia
- Constellation Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Robert M Campbell
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285
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397
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Schuster S, Roessler C, Meleshin M, Zimmermann P, Simic Z, Kambach C, Schiene-Fischer C, Steegborn C, Hottiger MO, Schutkowski M. A continuous sirtuin activity assay without any coupling to enzymatic or chemical reactions. Sci Rep 2016; 6:22643. [PMID: 26940860 PMCID: PMC4778124 DOI: 10.1038/srep22643] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 02/16/2016] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are NAD(+) dependent lysine deacylases involved in many regulatory processes such as control of metabolic pathways, DNA repair and stress response. Modulators of sirtuin activity are required as tools for uncovering the biological function of these enzymes and as potential therapeutic agents. Systematic discovery of such modulators is hampered by the lack of direct and continuous activity assays. The present study describes a novel continuous assay based on the increase of a fluorescence signal subsequent to sirtuin mediated removal of a fluorescent acyl chain from a modified TNFα-derived peptide. This substrate is well recognized by human sirtuins 1-6 and represents the best sirtuin 2 substrate described so far with a kcat/KM-value of 176 000 M(-1)s(-1). These extraordinary substrate properties allow the first determination of Ki-values for the specific Sirt2 inhibitory peptide S2iL5 (600 nM) and for the quasi-universal sirtuin inhibitor peptide thioxo myristoyl TNFα (80 nM).
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Affiliation(s)
- Sabine Schuster
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Claudia Roessler
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Philipp Zimmermann
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Christian Kambach
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, joint research project gFP5, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Michael O Hottiger
- IVBMB, University of Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 0610 Halle (Saale), Germany
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398
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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399
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Osamor VC, Chinedu SN, Azuh DE, Iweala EJ, Ogunlana OO. The interplay of post-translational modification and gene therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:861-71. [PMID: 27013864 PMCID: PMC4778776 DOI: 10.2147/dddt.s80496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Several proteins interact either to activate or repress the expression of other genes during transcription. Based on the impact of these activities, the proteins can be classified into readers, modifier writers, and modifier erasers depending on whether histone marks are read, added, or removed, respectively, from a specific amino acid. Transcription is controlled by dynamic epigenetic marks with serious health implications in certain complex diseases, whose understanding may be useful in gene therapy. This work highlights traditional and current advances in post-translational modifications with relevance to gene therapy delivery. We report that enhanced understanding of epigenetic machinery provides clues to functional implication of certain genes/gene products and may facilitate transition toward revision of our clinical treatment procedure with effective fortification of gene therapy delivery.
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Affiliation(s)
- Victor Chukwudi Osamor
- Covenant University Bioinformatics Research (CUBRe) Unit, Department of Computer and Information Sciences, College of Science and Technology (CST), Covenant University, Ota, Ogun State, Nigeria; Institute of Informatics (Computational biology and Bioinformatics), Faculty of Mathematics, Informatics and Mechanics, University of Warsaw (Uniwersytet Warszawski), Warszawa, Poland; Covenant University Public Health and Well-being Research Group (CUPHWERG), Covenant University, Canaan Land, Nigeria
| | - Shalom N Chinedu
- Covenant University Public Health and Well-being Research Group (CUPHWERG), Covenant University, Canaan Land, Nigeria; Biochemistry and Molecular Biology Unit, Department of Biological Sciences, College of Science and Technology, Covenant University, Canaan Land, Nigeria
| | - Dominic E Azuh
- Covenant University Public Health and Well-being Research Group (CUPHWERG), Covenant University, Canaan Land, Nigeria; Department of Economics and Development Studies, Covenant University, Ota, Ogun State, Nigeria
| | - Emeka Joshua Iweala
- Covenant University Public Health and Well-being Research Group (CUPHWERG), Covenant University, Canaan Land, Nigeria; Biochemistry and Molecular Biology Unit, Department of Biological Sciences, College of Science and Technology, Covenant University, Canaan Land, Nigeria
| | - Olubanke Olujoke Ogunlana
- Covenant University Public Health and Well-being Research Group (CUPHWERG), Covenant University, Canaan Land, Nigeria; Biochemistry and Molecular Biology Unit, Department of Biological Sciences, College of Science and Technology, Covenant University, Canaan Land, Nigeria
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400
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Nwasike C, Ewert S, Jovanovic S, Haider S, Mujtaba S. SET domain-mediated lysine methylation in lower organisms regulates growth and transcription in hosts. Ann N Y Acad Sci 2016; 1376:18-28. [PMID: 26919042 DOI: 10.1111/nyas.13017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 12/16/2022]
Abstract
Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain-mediated lysine methylation, one of the major epigenetic marks, has been found to regulate chromatin-mediated gene transcription. Published studies have established further that methylation is not restricted to nuclear proteins but is involved in many cellular processes, including growth, differentiation, immune regulation, and cancer progression. The biological complexity of lysine methylation emerges from its capacity to cause gene activation or gene repression owing to the specific position of methylated-lysine moieties on the chromatin. Accumulating evidence suggests that despite the absence of chromatin, viruses and prokaryotes also express SET proteins, although their functional roles remain relatively less investigated. One possibility could be that SET proteins in lower organisms have more than one biological function, for example, in regulating growth or in manipulating host transcription machinery in order to establish infection. Thus, elucidating the role of an SET protein in host-pathogen interactions requires a thorough understanding of their functions. This review discusses the biological role of lysine methylation in prokaryotes and lower eukaryotes, as well as the underlying structural complexity and functional diversity of SET proteins.
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Affiliation(s)
| | - Sinead Ewert
- UCL School of Pharmacy, University College London, London, United Kingdom
| | - Srdan Jovanovic
- UCL School of Pharmacy, University College London, London, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London, United Kingdom.
| | - Shiraz Mujtaba
- City University of New York, Medgar Evers College, Brooklyn, New York.
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