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Yan L, Li J, Hu J, Qu J, Li K, Wang M, An SS, Ke CC, Li H, Yuan F, Guo W, Hu M, Zhang J, Yang Z, Mu H, zhang F, Zhang J, Cui X, Hu Y. Biotin attenuates heat shock factor 4b transcriptional activity by lysine 444 biotinylation. Biochem Biophys Rep 2022; 30:101227. [PMID: 35198740 PMCID: PMC8841385 DOI: 10.1016/j.bbrep.2022.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/16/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic mutations in HSF4 cause congenital cataracts. HSF4 exhibits both positive and negative regulation on the transcription of heat shock and non-heat shock proteins during lens development, and its activity is regulated by posttranslational modifications. Biotin is an essential vitamin that regulates gene expression through protein biotinylation. In this paper, we report that HSF4b is negatively regulated by biotinylation. Administration of biotin or ectopic bacterial biotin ligase BirA increases HSF4b biotinylation at its C-terminal amino acids from 196 to 493. This attenuates the HSF4b-controlled expression of αB-crystallin in both lens epithelial cells and tested HEK293T cells. HSF4b interacts with holocarboxylase synthetase (HCS), a ubiquitous enzyme for catalyzing protein biotinylation in mammal. Ectopic HA-HCS expression downregulates HSF4b-controlled αB-crystallin expression. Lysine-mutation analyses indicate that HSF4b/K444 is a potential biotinylation site. Mutation K444R reduces the co-precipitation of HSF4b by streptavidin beads and biotin-induced reduction of αB-crystallin expression. Mutations of other lysine residues such as K207R/K209R, K225R, K288R, K294R and K355R in HSF4's C-terminal region do not affect HSF4's expression level and the interaction with streptavidin, but they exhibit distinct regulation on αB-crystallin expression through different mechanisms. HSF4/K294R leads to upregulation of αB-crystallin expression, while mutations K207R/K209R, K225R, K288R, K255R and K435R attenuate HSF4's regulation on αB-crystallin expression. K207R/K209R blocks HSF4 nuclear translocation, and K345R causes HSF4 destabilization. Taken together, the data reveal that biotin maybe a novel factor in modulating HSF4 activity through biotinylation. Biotin downregulates HSF4's transcription activity. HSF4 is associated with and down-regulated by holocarboxylase synthetase (HCS). K444 is the potential biotinylated amino acid residue in HSF4b.
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Affiliation(s)
- Longjun Yan
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Jing Li
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Jialin Hu
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Junwei Qu
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Kejia Li
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Mingli Wang
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Shuang-Shuang An
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Cun-cun Ke
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Hui Li
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Fengling Yuan
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Weikai Guo
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Mengyue Hu
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Jing Zhang
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Zhengyan Yang
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Hongmei Mu
- Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China
| | - Fengyan zhang
- Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhang
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
| | - Xiukun Cui
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
- Corresponding author.
| | - Yanzhong Hu
- National-Joint Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan International Union Lab of Antibody Medicine, Department of Cell Biology and Genetics, Henan University School of Basic Medical Sciences, Kaifeng, China
- Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China
- Corresponding author. Department of Cell Biology, Henan University School of Medicine, Zhengzhou, China.
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Sadri M, Wang H, Kuroishi T, Li Y, Zempleni J. Holocarboxylase synthetase knockout is embryonic lethal in mice. PLoS One 2022; 17:e0265539. [PMID: 35385533 PMCID: PMC8985998 DOI: 10.1371/journal.pone.0265539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the biotinylation of five distinct biotin-dependent carboxylases and perhaps chromatin proteins. HLCS deficiency causes multiple carboxylase deficiency which results in fatal consequences unless patients are diagnosed early and treated with pharmacological doses of biotin. The objective of this study was to develop an HLCS conditional knockout (KO) mouse and assess effects of HLCS knockout on embryo survival. In the mouse, exon 8 is flanked by LoxP sites, thereby removing a catalytically important region upon recombination by Cre. HLCS conditional KO mice were backcrossed for 14 generations with C57BL/6J mice to yield Hlcstm1Jze. Fertility and weight gain were normal and no frank disease phenotypes and abnormal feeding behavior were observed in the absence of Cre. HLCS knockout was embryonic lethal when dams homozygous for both the floxed Hlcs gene and tamoxifen-inducible Cre recombinase (denoted Hlcstm1.1Jze) were injected with tamoxifen on gestational days 2.5 and 10.5. This is the first report of an HLCS conditional KO mouse, which enables studies of the roles of HLCS and biotin in intermediary metabolism.
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Affiliation(s)
- Mahrou Sadri
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Haichuan Wang
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Toshinobu Kuroishi
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Yong Li
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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Herlihy CP, Hahn S, Hermance NM, Crowley EA, Manning AL. Suv420 enrichment at the centromere limits Aurora B localization and function. J Cell Sci 2021; 134:jcs249763. [PMID: 34342353 PMCID: PMC8353524 DOI: 10.1242/jcs.249763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Centromere structure and function are defined by the epigenetic modification of histones at centromeric and pericentromeric chromatin. The constitutive heterochromatin found at pericentromeric regions is highly enriched for H3K9me3 and H4K20me3. Although mis-expression of the methyltransferase enzymes that regulate these marks, Suv39 and Suv420, is common in disease, the consequences of such changes are not well understood. Our data show that increased centromere localization of Suv39 and Suv420 suppresses centromere transcription and compromises localization of the mitotic kinase Aurora B, decreasing microtubule dynamics and compromising chromosome alignment and segregation. We find that inhibition of Suv420 methyltransferase activity partially restores Aurora B localization to centromeres and that restoration of the Aurora B-containing chromosomal passenger complex to the centromere is sufficient to suppress mitotic errors that result when Suv420 and H4K20me3 is enriched at centromeres. Consistent with a role for Suv39 and Suv420 in negatively regulating Aurora B, high expression of these enzymes corresponds with increased sensitivity to Aurora kinase inhibition in human cancer cells, suggesting that increased H3K9 and H4K20 methylation may be an underappreciated source of chromosome mis-segregation in cancer. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | | | | | | | - Amity L. Manning
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609USA
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D'Mello SR. MECP2 and the Biology of MECP2 Duplication Syndrome. J Neurochem 2021; 159:29-60. [PMID: 33638179 DOI: 10.1111/jnc.15331] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 11/27/2022]
Abstract
MECP2 duplication syndrome (MDS), a rare X-linked genomic disorder affecting predominantly males, is caused by duplication of the chromosomal region containing the methyl CpG binding protein-2 (MECP2) gene, which encodes methyl-CpG-binding protein 2 (MECP2), a multi-functional protein required for proper brain development and maintenance of brain function during adulthood. Disease symptoms include severe motor and cognitive impairment, delayed or absent speech development, autistic features, seizures, ataxia, recurrent respiratory infections and shortened lifespan. The cellular and molecular mechanisms by which a relatively modest increase in MECP2 protein causes such severe disease symptoms are poorly understood and consequently there are no treatments available for this fatal disorder. This review summarizes what is known to date about the structure and complex regulation of MECP2 and its many functions in the developing and adult brain. Additionally, recent experimental findings on the cellular and molecular underpinnings of MDS based on cell culture and mouse models of the disorder are reviewed. The emerging picture from these studies is that MDS is a neurodegenerative disorder in which neurons die in specific parts of the central nervous system, including the cortex, hippocampus, cerebellum and spinal cord. Neuronal death likely results from astrocytic dysfunction, including a breakdown of glutamate homeostatic mechanisms. The role of elevations in the expression of glial acidic fibrillary protein (GFAP) in astrocytes and the microtubule-associated protein, Tau, in neurons to the pathogenesis of MDS is discussed. Lastly, potential therapeutic strategies to potentially treat MDS are discussed.
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Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
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Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Tillotson R, Bird A. The Molecular Basis of MeCP2 Function in the Brain. J Mol Biol 2020; 432:1602-1623. [PMID: 31629770 DOI: 10.1016/j.jmb.2019.10.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/14/2022]
Abstract
MeCP2 is a reader of the DNA methylome that occupies a large proportion of the genome due to its high abundance and the frequency of its target sites. It has been the subject of extensive study because of its link with 'MECP2-related disorders', of which Rett syndrome is the most prevalent. This review integrates evidence from patient mutation data with results of experimental studies using mouse models, cell lines and in vitro systems to critically evaluate our understanding of MeCP2 protein function. Recent evidence challenges the idea that MeCP2 is a multifunctional hub that integrates diverse processes to underpin neuronal function, suggesting instead that its primary role is to recruit the NCoR1/2 co-repressor complex to methylated sites in the genome, leading to dampening of gene expression.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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Liu L, Ling X, Wu M, Chen J, Chen S, Tan Q, Chen J, Liu J, Zou F. Rb silencing mediated by the down-regulation of MeCP2 is involved in cell transformation induced by long-term exposure to hydroquinone. Mol Carcinog 2016; 56:651-663. [DOI: 10.1002/mc.22523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/04/2016] [Accepted: 07/01/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Linhua Liu
- Department of Occupational Health and Occupational Medicine; Guangdong Provincial Key Laboratory of Tropical Disease Research; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou PR China
- Department of Environmental and Occupational Health; Dongguan Key Laboratory of Environmental Medicine; School of Public Health; Guangdong Medical University; Dongguan PR China
| | - Xiaoxuan Ling
- Department of Environmental and Occupational Health; Dongguan Key Laboratory of Environmental Medicine; School of Public Health; Guangdong Medical University; Dongguan PR China
- School of Public Health; Guangzhou Medical University; Guangzhou PR China
| | - Minhua Wu
- Department of Histology and Embryology; Guangdong Medical University; Zhanjiang PR China
| | - Jialong Chen
- Department of Occupational Health and Occupational Medicine; Guangdong Provincial Key Laboratory of Tropical Disease Research; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou PR China
- Department of Environmental and Occupational Health; Dongguan Key Laboratory of Environmental Medicine; School of Public Health; Guangdong Medical University; Dongguan PR China
| | - Shaoqiao Chen
- Department of Clinical Laboratory; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou PR China
| | - Qiang Tan
- Foshan Institute of Occupational Disease Prevention and Control; Foshan PR China
| | - Jiansong Chen
- School of Public Health; Guangzhou Medical University; Guangzhou PR China
| | - Jiaxian Liu
- Department of Environmental and Occupational Health; Dongguan Key Laboratory of Environmental Medicine; School of Public Health; Guangdong Medical University; Dongguan PR China
| | - Fei Zou
- Department of Occupational Health and Occupational Medicine; Guangdong Provincial Key Laboratory of Tropical Disease Research; School of Public Health and Tropical Medicine; Southern Medical University; Guangzhou PR China
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Cordonier EL, Adjam R, Teixeira DC, Onur S, Zbasnik R, Read PE, Döring F, Schlegel VL, Zempleni J. Resveratrol compounds inhibit human holocarboxylase synthetase and cause a lean phenotype in Drosophila melanogaster. J Nutr Biochem 2015; 26:1379-84. [PMID: 26303405 DOI: 10.1016/j.jnutbio.2015.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/22/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023]
Abstract
Holocarboxylase synthetase (HLCS) is the sole protein-biotin ligase in the human proteome. HLCS has key regulatory functions in intermediary metabolism, including fatty acid metabolism, and in gene repression through epigenetic mechanisms. The objective of this study was to identify food-borne inhibitors of HLCS that alter HLCS-dependent pathways in metabolism and gene regulation. When libraries of extracts from natural products and chemically pure compounds were screened for HLCS inhibitor activity, resveratrol compounds in grape materials caused an HLCS inhibition of >98% in vitro. The potency of these compounds was piceatannol>resveratrol>piceid. Grape-borne compounds other than resveratrol metabolites also contributed toward HLCS inhibition, e.g., p-coumaric acid and cyanidin chloride. HLCS inhibitors had meaningful effects on body fat mass. When Drosophila melanogaster brummer mutants, which are genetically predisposed to storing excess amounts of lipids, were fed diets enriched with grape leaf extracts and piceid, body fat mass decreased by more than 30% in males and females. However, Drosophila responded to inhibitor treatment with an increase in the expression of HLCS, which elicited an increase in the abundance of biotinylated carboxylases in vivo. We conclude that mechanisms other than inhibition of HLCS cause body fat loss in flies. We propose that the primary candidate is the inhibition of the insulin receptor/Akt signaling pathway.
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Affiliation(s)
- Elizabeth L Cordonier
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 316 Ruth Leverton Hall, Lincoln, NE 68583-0806, USA
| | - Riem Adjam
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 316 Ruth Leverton Hall, Lincoln, NE 68583-0806, USA
| | - Daniel Camara Teixeira
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 316 Ruth Leverton Hall, Lincoln, NE 68583-0806, USA
| | - Simone Onur
- Abteilung Molekulare Prävention, Institut für Humanernährung und Lebensmittelkunde, Universität Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Richard Zbasnik
- Department of Food Science and Technology, University of Nebraska-Lincoln, 326 Filley Hall, Lincoln, NE 68583-0806, USA
| | - Paul E Read
- Department of Agronomy, University of Nebraska-Lincoln, 377 Plant Science Hall, Lincoln, NE 68583-0724, USA
| | - Frank Döring
- Abteilung Molekulare Prävention, Institut für Humanernährung und Lebensmittelkunde, Universität Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Vicki L Schlegel
- Department of Food Science and Technology, University of Nebraska-Lincoln, 326 Filley Hall, Lincoln, NE 68583-0806, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, 316 Ruth Leverton Hall, Lincoln, NE 68583-0806, USA.
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Abstract
Rett syndrome (RTT) is a severe neurological disorder caused by mutations in the X-linked gene MECP2 (methyl-CpG-binding protein 2). Two decades of research have fostered the view that MeCP2 is a multifunctional chromatin protein that integrates diverse aspects of neuronal biology. More recently, studies have focused on specific RTT-associated mutations within the protein. This work has yielded molecular insights into the critical functions of MeCP2 that promise to simplify our understanding of RTT pathology.
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Affiliation(s)
- Matthew J Lyst
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Adrian Bird
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
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Tao H, Yang JJ, Shi KH. Non-coding RNAs as direct and indirect modulators of epigenetic mechanism regulation of cardiac fibrosis. Expert Opin Ther Targets 2015; 19:707-16. [PMID: 25652534 DOI: 10.1517/14728222.2014.1001740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Cardiac fibroblast activation is a pivotal cellular event in cardiac fibrosis. Numerous studies have indicated that epigenetic modifications control cardiac fibroblast activation. Greater knowledge of the role of epigenetic modifications could improve understanding of the cardiac fibrosis pathogenesis. AREAS COVERED The aim of this review is to describe the present knowledge about the important role of non-coding RNA (ncRNA) transcripts in epigenetic gene regulation in cardiac fibrosis and looks ahead on new perspectives of epigenetic modification research. Furthermore, we will discuss examples of ncRNAs that interact with histone modification or DNA methylation to regulate gene expression. EXPERT OPINION MicroRNAs (miRNAs) and long ncRNAs (lncRNAs) modulate several important aspects of function. Recently, some studies continue to find novel pathways, including the important role of ncRNA transcripts in epigenetic gene regulation. Targeting the miRNAs and lncRNAs can be a promising direction in cardiac fibrosis treatment. We discuss new perspectives of ncRNAs that interact with histone modification or DNA methylation to regulate gene expression, others that are targets of these epigenetic mechanisms. The emerging recognition of the diverse functions of ncRNAs in regulating gene expression by epigenetic mechanisms suggests that they may represent new targets for therapeutic intervention.
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Affiliation(s)
- Hui Tao
- The Second Hospital of Anhui Medical University, Department of Cardiothoracic Surgery , Fu Rong Road, Hefei 230601, Anhui Province , China +86 551 63869531 ; +86 551 63869531 ;
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11
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Montague E, Janko I, Stanberry L, Lee E, Choiniere J, Anderson N, Stewart E, Broomall W, Higdon R, Kolker N, Kolker E. Beyond protein expression, MOPED goes multi-omics. Nucleic Acids Res 2014; 43:D1145-51. [PMID: 25404128 PMCID: PMC4383969 DOI: 10.1093/nar/gku1175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
MOPED (Multi-Omics Profiling Expression Database; http://moped.proteinspire.org) has transitioned from solely a protein expression database to a multi-omics resource for human and model organisms. Through a web-based interface, MOPED presents consistently processed data for gene, protein and pathway expression. To improve data quality, consistency and use, MOPED includes metadata detailing experimental design and analysis methods. The multi-omics data are integrated through direct links between genes and proteins and further connected to pathways and experiments. MOPED now contains over 5 million records, information for approximately 75 000 genes and 50 000 proteins from four organisms (human, mouse, worm, yeast). These records correspond to 670 unique combinations of experiment, condition, localization and tissue. MOPED includes the following new features: pathway expression, Pathway Details pages, experimental metadata checklists, experiment summary statistics and more advanced searching tools. Advanced searching enables querying for genes, proteins, experiments, pathways and keywords of interest. The system is enhanced with visualizations for comparing across different data types. In the future MOPED will expand the number of organisms, increase integration with pathways and provide connections to disease.
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Affiliation(s)
- Elizabeth Montague
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Imre Janko
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Larissa Stanberry
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Elaine Lee
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - John Choiniere
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Nathaniel Anderson
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Elizabeth Stewart
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - William Broomall
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Roger Higdon
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Natali Kolker
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101
| | - Eugene Kolker
- Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101 Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, WA, USA 98109 Department of Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, MA 02115
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12
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Sittiwong W, Cordonier EL, Zempleni J, Dussault PH. β-Keto and β-hydroxyphosphonate analogs of biotin-5'-AMP are inhibitors of holocarboxylase synthetase. Bioorg Med Chem Lett 2014; 24:5568-5571. [PMID: 25466176 DOI: 10.1016/j.bmcl.2014.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin to cytoplasmic and mitochondrial carboxylases, nuclear histones, and over a hundred human proteins. Nonhydrolyzable ketophosphonate (β-ketoP) and hydroxyphosphonate (β-hydroxyP) analogs of biotin-5'-AMP inhibit holocarboxylase synthetase (HLCS) with IC50 values of 39.7 μM and 203.7 μM. By comparison, an IC50 value of 7 μM was observed with the previously reported biotinol-5'-AMP. The Ki values, 3.4 μM and 17.3 μM, respectively, are consistent with the IC50 results, and close to the Ki obtained for biotinol-5'-AMP (7 μM). The β-ketoP and β-hydroxyP molecules are competitive inhibitors of HLCS while biotinol-5'-AMP inhibited HLCS by a mixed mechanism.
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Affiliation(s)
- Wantanee Sittiwong
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Elizabeth L Cordonier
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA.
| | - Patrick H Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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13
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Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats. Biochem J 2014; 461:477-86. [PMID: 24840043 DOI: 10.1042/bj20131208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HLCS (holocarboxylase synthetase) is a nuclear protein that catalyses the binding of biotin to distinct lysine residues in chromatin proteins. HLCS-dependent epigenetic marks are over-represented in repressed genomic loci, particularly in repeats. Evidence is mounting that HLCS is a member of a multi-protein gene repression complex, which determines its localization in chromatin. In the present study we tested the hypothesis that HLCS interacts physically with N-CoR (nuclear receptor co-repressor) and HDAC1 (histone deacetylase 1), thereby contributing toward the removal of H3K9ac (Lys⁹-acetylated histone H3) gene activation marks and the repression of repeats. Physical interactions between HLCS and N-CoR, HDAC1 and a novel splicing variant of HDAC1 were confirmed by co-immunoprecipitation, limited proteolysis and split luciferase complementation assays. When HLCS was overexpressed, the abundance of H3K9ac marks decreased by 50% and 68% in LTRs (long terminal repeats) 15 and 22 respectively in HEK (human embryonic kidney)-293 cells compared with the controls. This loss of H3K9ac marks was linked with an 83% decrease in mRNA coding for LTRs. Similar patterns were seen in pericentromeric alpha satellite repeats in chromosomes 1 and 4. We conclude that interactions of HLCS with N-CoR and HDACs contribute towards the transcriptional repression of repeats, presumably increasing genome stability.
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14
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Romagnolo DF, Zempleni J, Selmin OI. Nuclear receptors and epigenetic regulation: opportunities for nutritional targeting and disease prevention. Adv Nutr 2014; 5:373-85. [PMID: 25022987 PMCID: PMC4085186 DOI: 10.3945/an.114.005868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Posttranslational modifications of histones, alterations in the recruitment and functions of non-histone proteins, DNA methylation, and changes in expression of noncoding RNAs contribute to current models of epigenetic regulation. Nuclear receptors (NRs) are a group of transcription factors that, through ligand-binding, act as sensors to changes in nutritional, environmental, developmental, pathophysiologic, and endocrine conditions and drive adaptive responses via gene regulation. One mechanism through which NRs direct gene expression is the assembly of transcription complexes with cofactors and coregulators that possess chromatin-modifying properties. Chromatin modifications can be transient or become part of the cellular "memory" and contribute to genomic imprinting. Because many food components bind to NRs, they can ultimately influence transcription of genes associated with biologic processes, such as inflammation, proliferation, apoptosis, and hormonal response, and alter the susceptibility to chronic diseases (e.g., cancer, diabetes, obesity). The objective of this review is to highlight how NRs influence epigenetic regulation and the relevance of dietary compound-NR interactions in human nutrition and for disease prevention and treatment. Identifying gene targets of unliganded and bound NRs may assist in the development of epigenetic maps for food components and dietary patterns. Progress in these areas may lead to the formulation of disease-prevention models based on epigenetic control by individual or associations of food ligands of NRs.
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Affiliation(s)
- Donato F Romagnolo
- Department of Nutritional Sciences and University of Arizona Cancer Center, University of Arizona, Tucson, AZ; and
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Ornella I Selmin
- Department of Nutritional Sciences and University of Arizona Cancer Center, University of Arizona, Tucson, AZ; and
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15
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Zempleni J, Liu D, Camara DT, Cordonier EL. Novel roles of holocarboxylase synthetase in gene regulation and intermediary metabolism. Nutr Rev 2014; 72:369-76. [PMID: 24684412 DOI: 10.1111/nure.12103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The role of holocarboxylase synthetase (HLCS) in catalyzing the covalent binding of biotin to the five biotin-dependent carboxylases in humans is well established, as are the essential roles of these carboxylases in the metabolism of fatty acids, the catabolism of leucine, and gluconeogenesis. This review examines recent discoveries regarding the roles of HLCS in assembling a multiprotein gene repression complex in chromatin. In addition, emerging evidence suggests that the number of biotinylated proteins is far larger than previously assumed and includes members of the heat-shock superfamily of proteins and proteins coded by the ENO1 gene. Evidence is presented linking biotinylation of heat-shock proteins HSP60 and HSP72 with redox biology and immune function, respectively, and biotinylation of the two ENO1 gene products MBP-1 and ENO1 with tumor suppression and glycolysis, respectively.
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Affiliation(s)
- Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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16
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Kleefstra T, Schenck A, Kramer JM, van Bokhoven H. The genetics of cognitive epigenetics. Neuropharmacology 2014; 80:83-94. [PMID: 24434855 DOI: 10.1016/j.neuropharm.2013.12.025] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 01/31/2023]
Abstract
Cognitive disorders (CDs) are a heterogeneous group of disorders for which the genetic foundations are rapidly being uncovered. The large number of CD-associated gene mutations presents an opportunity to identify common mechanisms of disease as well as molecular processes that are of key importance to human cognition. Given the disproportionately high number of epigenetic genes associated with CD, epigenetic regulation of gene transcription is emerging as a process of major importance in cognition. The cognate protein products of these genes often co-operate in shared protein complexes or pathways, which is reflected in similarities between the neurodevelopmental phenotypes corresponding to these mutant genes. Here we provide an overview of the genes associated with CDs, and highlight some of the epigenetic regulatory complexes involving multiple CD genes. Such common gene networks may provide a handle for designing therapeutic interventions applicable to a number of cognitive disorders with variable genetic etiology.
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Affiliation(s)
- Tjitske Kleefstra
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Annette Schenck
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Jamie M Kramer
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands; Radboud University Medical Center, Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
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17
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Xue J, Zempleni J. Epigenetic synergies between biotin and folate in the regulation of pro-inflammatory cytokines and repeats. Scand J Immunol 2014; 78:419-25. [PMID: 24007195 DOI: 10.1111/sji.12108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/30/2013] [Indexed: 12/29/2022]
Abstract
The protein biotin ligase, holocarboxylase synthetase (HLCS), is a chromatin protein that interacts physically with the DNA methyltransferase DNMT1, the methylated cytosine-binding protein MeCP2 and the histone H3 K9-methyltransferase EHMT1, all of which participate in folate-dependent gene repression. Here we tested the hypothesis that biotin and folate synergize in the repression of pro-inflammatory cytokines and long-terminal repeats (LTRs), mediated by interactions between HLCS and other chromatin proteins. Biotin and folate supplementation could compensate for each other's deficiency in the repression of LTRs in Jurkat and U937 cells. For example, when biotin-deficient Jurkat cells were supplemented with folate, the expression of LTRs decreased by >70%. Epigenetic synergies were more complex in the regulation of cytokines compared with LTRs. For example, the abundance of TNF-α was 100% greater in folate- and biotin-supplemented U937 cells compared with biotin-deficient and folate-supplemented cells. The NF-κB inhibitor curcumin abrogated the effects of folate and biotin in cytokine regulation, suggesting that transcription factor signalling adds an extra layer of complexity to the regulation of cytokine genes by epigenetic phenomena. We conclude that biotin and folate synergize in the repression of LTRs and that these interactions are probably mediated by HLCS-dependent epigenetic mechanisms. In contrast, synergies between biotin and folate in the regulation of cytokines need to be interpreted in the context of transcription factor signalling.
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Affiliation(s)
- J Xue
- Department of Nutrition and Health Sciences, University of Nebraska at Lincoln, Lincoln, NE, USA
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18
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Health promoting effects of brassica-derived phytochemicals: from chemopreventive and anti-inflammatory activities to epigenetic regulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:964539. [PMID: 24454992 PMCID: PMC3885109 DOI: 10.1155/2013/964539] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/20/2013] [Indexed: 12/19/2022]
Abstract
A high intake of brassica vegetables may be associated with a decreased chronic disease risk. Health promoting effects of Brassicaceae have been partly attributed to glucosinolates and in particular to their hydrolyzation products including isothiocyanates. In vitro and in vivo studies suggest a chemopreventive activity of isothiocyanates through the redox-sensitive transcription factor Nrf2. Furthermore, studies in cultured cells, in laboratory rodents, and also in humans support an anti-inflammatory effect of brassica-derived phytochemicals. However, the underlying mechanisms of how these compounds mediate their health promoting effects are yet not fully understood. Recent findings suggest that brassica-derived compounds are regulators of epigenetic mechanisms. It has been shown that isothiocyanates may inhibit histone deacetylase transferases and DNA-methyltransferases in cultured cells. Only a few papers have dealt with the effect of brassica-derived compounds on epigenetic mechanisms in laboratory animals, whereas data in humans are currently lacking. The present review aims to summarize the current knowledge regarding the biological activities of brassica-derived phytochemicals regarding chemopreventive, anti-inflammatory, and epigenetic pathways.
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19
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Xue J, Zhou J, Zempleni J. Holocarboxylase synthetase catalyzes biotinylation of heat shock protein 72, thereby inducing RANTES expression in HEK-293 cells. Am J Physiol Cell Physiol 2013; 305:C1240-5. [PMID: 24133061 DOI: 10.1152/ajpcell.00279.2013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a recent mass spectrometry screen, we identified 108 new proteins that were modified endogenously by covalent binding of biotin; members of the heat shock superfamily of proteins, including heat shock protein 72 (HSP72), were overrepresented among the biotinylated proteins. Mammals respond to infections by secreting extracellular HSP72 (eHSP72), which elicits an immune response. Here, using mass spectrometry and site-directed mutagenesis, we identified five biotinylation sites in HSP72. We used coimmunoprecipitation, mass spectrometry, and limited proteolysis assays to demonstrate that HSP72 interacts physically with the protein biotin ligase holocarboxylase synthetase (HLCS), leading to biotinylation of residues K112, K128 K348, K361, K415, and, probably, additional lysines. Finally, we demonstrated that HLCS-dependent biotinylation of eHSP72 increases expression of the chemokine regulated on activation normal T-expressed and presumably secreted (RANTES) by human embryonic kidney (HEK-293) cells. In conclusion, we report a novel endogenous modification of HSP72 and demonstrated that binding of biotin to eHSP72 prepares cells for a strong immune response.
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Affiliation(s)
- Jing Xue
- Department of Nutrition and Health Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska
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