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Tarbet HJ, Dolat L, Smith TJ, Condon BM, O'Brien ET, Valdivia RH, Boyce M. Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton. eLife 2018. [PMID: 29513221 PMCID: PMC5841932 DOI: 10.7554/elife.31807] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Intermediate filaments (IF) are a major component of the metazoan cytoskeleton and are essential for normal cell morphology, motility, and signal transduction. Dysregulation of IFs causes a wide range of human diseases, including skin disorders, cardiomyopathies, lipodystrophy, and neuropathy. Despite this pathophysiological significance, how cells regulate IF structure, dynamics, and function remains poorly understood. Here, we show that site-specific modification of the prototypical IF protein vimentin with O-linked β-N-acetylglucosamine (O-GlcNAc) mediates its homotypic protein-protein interactions and is required in human cells for IF morphology and cell migration. In addition, we show that the intracellular pathogen Chlamydia trachomatis, which remodels the host IF cytoskeleton during infection, requires specific vimentin glycosylation sites and O-GlcNAc transferase activity to maintain its replicative niche. Our results provide new insight into the biochemical and cell biological functions of vimentin O-GlcNAcylation, and may have broad implications for our understanding of the regulation of IF proteins in general. Like the body's skeleton, the cytoskeleton gives shape and structure to the inside of a cell. Yet, unlike a skeleton, the cytoskeleton is ever changing. The cytoskeleton consists of many fibers each made from chains of protein molecules. One of these proteins is called vimentin and it forms intermediate filaments in the cytoskeleton. Many different types of cells contain vimentin and a lot of it is found in cancer cells that have spread beyond their original location to other sites in the body. Cells use chemical modifications to regulate cytoskeleton proteins. For example, through a process called glycosylation, cells can reversibly attach a sugar modification called O-GlcNAc to vimentin. O-GlcNAc can be attached to several different parts of vimentin and each location may have a different effect. It is not currently clear how cells control their vimentin filaments or what role O-GlcNAc plays in this process. Using genetic engineering, Tarbet et al. produced human cells in the laboratory with modified vimentin proteins. These altered proteins lacked some of the sites for O-GlcNAc attachment. The goal was to see whether the loss of O-GlcNAc at a specific location would affect fiber formation and cell behavior. The results showed one site where vimentin needs O-GlcNAc to form fibers. Without O-GlcNAc at this site, cells could not migrate towards chemical signals. In addition, in normal human cells, Chlamydia bacteria hijack vimentin and rearrange the filaments to form a cage around themselves for protection. However, the cells lacking O-GlcNAc on vimentin were resistant to infection by Chlamydia bacteria. These findings highlight the importance of O-GlcNAc on vimentin in healthy cells and during infection. Vimentin’s contribution to cell migration may also help to explain its role in the spread of cancer. The importance of O-GlcNAc suggests it could be a new target for therapies. Yet, it also highlights the need for caution due to the delicate balance between the activity of vimentin in healthy and diseased cells. In addition, human cells produce about 70 other vimentin-like proteins and further work will examine if they are also affected by O-GlcNAc.
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Affiliation(s)
- Heather J Tarbet
- Department of Biochemistry, Duke University School of Medicine, Durham, United States
| | - Lee Dolat
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States.,Center for Host-Microbial Interactions, Duke University School of Medicine, Durham, United States
| | - Timothy J Smith
- Department of Biochemistry, Duke University School of Medicine, Durham, United States
| | - Brett M Condon
- Department of Biochemistry, Duke University School of Medicine, Durham, United States
| | - E Timothy O'Brien
- Department of Biochemistry, Duke University School of Medicine, Durham, United States.,Department of Physics and Astronomy, University of North Carolina, Chapel Hill, United States
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States.,Center for Host-Microbial Interactions, Duke University School of Medicine, Durham, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, United States.,Center for Host-Microbial Interactions, Duke University School of Medicine, Durham, United States
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102
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Shi H, Munk A, Nielsen TS, Daughtry MR, Larsson L, Li S, Høyer KF, Geisler HW, Sulek K, Kjøbsted R, Fisher T, Andersen MM, Shen Z, Hansen UK, England EM, Cheng Z, Højlund K, Wojtaszewski JFP, Yang X, Hulver MW, Helm RF, Treebak JT, Gerrard DE. Skeletal muscle O-GlcNAc transferase is important for muscle energy homeostasis and whole-body insulin sensitivity. Mol Metab 2018. [PMID: 29525407 PMCID: PMC6001359 DOI: 10.1016/j.molmet.2018.02.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective Given that cellular O-GlcNAcylation levels are thought to be real-time measures of cellular nutrient status and dysregulated O-GlcNAc signaling is associated with insulin resistance, we evaluated the role of O-GlcNAc transferase (OGT), the enzyme that mediates O-GlcNAcylation, in skeletal muscle. Methods We assessed O-GlcNAcylation levels in skeletal muscle from obese, type 2 diabetic people, and we characterized muscle-specific OGT knockout (mKO) mice in metabolic cages and measured energy expenditure and substrate utilization pattern using indirect calorimetry. Whole body insulin sensitivity was assessed using the hyperinsulinemic euglycemic clamp technique and tissue-specific glucose uptake was subsequently evaluated. Tissues were used for histology, qPCR, Western blot, co-immunoprecipitation, and chromatin immunoprecipitation analyses. Results We found elevated levels of O-GlcNAc-modified proteins in obese, type 2 diabetic people compared with well-matched obese and lean controls. Muscle-specific OGT knockout mice were lean, and whole body energy expenditure and insulin sensitivity were increased in these mice, consistent with enhanced glucose uptake and elevated glycolytic enzyme activities in skeletal muscle. Moreover, enhanced glucose uptake was also observed in white adipose tissue that was browner than that of WT mice. Interestingly, mKO mice had elevated mRNA levels of Il15 in skeletal muscle and increased circulating IL-15 levels. We found that OGT in muscle mediates transcriptional repression of Il15 by O-GlcNAcylating Enhancer of Zeste Homolog 2 (EZH2). Conclusions Elevated muscle O-GlcNAc levels paralleled insulin resistance and type 2 diabetes in humans. Moreover, OGT-mediated signaling is necessary for proper skeletal muscle metabolism and whole-body energy homeostasis, and our data highlight O-GlcNAcylation as a potential target for ameliorating metabolic disorders. Type 2 diabetic humans have elevated O-GlcNAc levels in skeletal muscle. Knockout of OGT in muscle elevates whole body insulin sensitivity. Knockout of OGT in muscle increases resistance to diet-induced obesity. Muscle-specific OGT knockout mice have elevated plasma IL-15 levels. OGT in muscle controls Il15 expression by O-GlcNAcylation and inhibition of EZH2.
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Affiliation(s)
- Hao Shi
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alexander Munk
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Thomas S Nielsen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Morgan R Daughtry
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Louise Larsson
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Shize Li
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kasper F Høyer
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark; Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, DK8000, Denmark
| | - Hannah W Geisler
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Karolina Sulek
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Rasmus Kjøbsted
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, DK2100, Denmark
| | - Taylor Fisher
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Marianne M Andersen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Zhengxing Shen
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ulrik K Hansen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Eric M England
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhiyong Cheng
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, Odense, Denmark; Section of Molecular Diabetes and Metabolism, Institute of Molecular Medicine and Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jørgen F P Wojtaszewski
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, DK2100, Denmark
| | - Xiaoyong Yang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Matthew W Hulver
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; The Virginia Tech Metabolic Phenotyping Core, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Jonas T Treebak
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark.
| | - David E Gerrard
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Shanmugam MK, Arfuso F, Arumugam S, Chinnathambi A, Jinsong B, Warrier S, Wang LZ, Kumar AP, Ahn KS, Sethi G, Lakshmanan M. Role of novel histone modifications in cancer. Oncotarget 2018; 9:11414-11426. [PMID: 29541423 PMCID: PMC5834259 DOI: 10.18632/oncotarget.23356] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/01/2017] [Indexed: 01/02/2023] Open
Abstract
Oncogenesis is a multistep process mediated by a variety of factors including epigenetic modifications. Global epigenetic post-translational modifications have been detected in almost all cancers types. Epigenetic changes appear briefly and do not involve permanent changes to the primary DNA sequence. These epigenetic modifications occur in key oncogenes, tumor suppressor genes, and transcription factors, leading to cancer initiation and progression. The most commonly observed epigenetic changes include DNA methylation, histone lysine methylation and demethylation, histone lysine acetylation and deacetylation. However, there are several other novel post-translational modifications that have been observed in recent times such as neddylation, sumoylation, glycosylation, phosphorylation, poly-ADP ribosylation, ubiquitination as well as transcriptional regulation and these have been briefly discussed in this article. We have also highlighted the diverse epigenetic changes that occur during the process of tumorigenesis and described the role of histone modifications that can occur on tumor suppressor genes as well as oncogenes, which regulate tumorigenesis and can thus form the basis of novel strategies for cancer therapy.
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Affiliation(s)
- Muthu K. Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Surendar Arumugam
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Bian Jinsong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, School of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, India
| | - Ling Zhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
- National University Cancer Institute, National University Health System, Singapore, Singapore
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
| | - Kwang Seok Ahn
- College of Korean Medicine, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
- Department of Pathology, National University Hospital Singapore, Singapore, Singapore
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104
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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105
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Parween S, Varghese DS, Ardah MT, Prabakaran AD, Mensah-Brown E, Emerald BS, Ansari SA. Higher O-GlcNAc Levels Are Associated with Defects in Progenitor Proliferation and Premature Neuronal Differentiation during in-Vitro Human Embryonic Cortical Neurogenesis. Front Cell Neurosci 2017; 11:415. [PMID: 29311838 PMCID: PMC5742625 DOI: 10.3389/fncel.2017.00415] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
The nutrient responsive O-GlcNAcylation is a dynamic post-translational protein modification found on several nucleocytoplasmic proteins. Previous studies have suggested that hyperglycemia induces the levels of total O-GlcNAcylation inside the cells. Hyperglycemia mediated increase in protein O-GlcNAcylation has been shown to be responsible for various pathologies including insulin resistance and Alzheimer's disease. Since maternal hyperglycemia during pregnancy is associated with adverse neurodevelopmental outcomes in the offspring, it is intriguing to identify the effect of increased protein O-GlcNAcylation on embryonic neurogenesis. Herein using human embryonic stem cells (hESCs) as model, we show that increased levels of total O-GlcNAc is associated with decreased neural progenitor proliferation and premature differentiation of cortical neurons, reduced AKT phosphorylation, increased apoptosis and defects in the expression of various regulators of embryonic corticogenesis. As defects in proliferation and differentiation during neurodevelopment are common features of various neurodevelopmental disorders, increased O-GlcNAcylation could be one mechanism responsible for defective neurodevelopmental outcomes in metabolically compromised pregnancies such as diabetes.
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Affiliation(s)
- Shama Parween
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya S Varghese
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mustafa T Ardah
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ashok D Prabakaran
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Eric Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Suraiya A Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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106
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"Nutrient-sensing" and self-renewal: O-GlcNAc in a new role. J Bioenerg Biomembr 2017; 50:205-211. [PMID: 29204729 DOI: 10.1007/s10863-017-9735-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/21/2017] [Indexed: 12/14/2022]
Abstract
Whether embryonic, hematopoietic or cancer stem cells, this metabolic reprogramming is dependent on the nutrient-status and bioenergetic pathways that is influenced by the micro-environmental niches like hypoxia. Thus, the microenvironment plays a vital role in determining the stem cell fate by inducing metabolic reprogramming. Under the influence of the microenvironment, like hypoxia, the stem cells have increased glucose and glutamine uptake which result in activation of hexosamine biosynthesis pathway (HBP) and increased O-GlcNAc Transferase (OGT). The current review is focused on understanding how HBP, a nutrient-sensing pathway (that leads to increased OGT activity) is instrumental in regulating self-renewal not only in embryonic and hematopoietic stem cells (ESC/HSC) but also in cancer stem cells.
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107
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Tarbet HJ, Toleman CA, Boyce M. A Sweet Embrace: Control of Protein-Protein Interactions by O-Linked β-N-Acetylglucosamine. Biochemistry 2017; 57:13-21. [PMID: 29099585 DOI: 10.1021/acs.biochem.7b00871] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
O-Linked β-N-acetylglucosamine (O-GlcNAc) is a critical post-translational modification (PTM) of thousands of intracellular proteins. Reversible O-GlcNAcylation governs many aspects of cell physiology and is dysregulated in numerous human diseases. Despite this broad pathophysiological significance, major aspects of O-GlcNAc signaling remain poorly understood, including the biochemical mechanisms through which O-GlcNAc transduces information. Recent work from many laboratories, including our own, has revealed that O-GlcNAc, like other intracellular PTMs, can control its substrates' functions by inhibiting or inducing protein-protein interactions. This dynamic regulation of multiprotein complexes exerts diverse downstream signaling effects in a range of processes, cell types, and organisms. Here, we review the literature about O-GlcNAc-regulated protein-protein interactions and suggest important questions for future studies in the field.
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Affiliation(s)
- Heather J Tarbet
- Department of Biochemistry, Duke University School of Medicine , Durham, North Carolina 27710, United States
| | - Clifford A Toleman
- Department of Biochemistry, Duke University School of Medicine , Durham, North Carolina 27710, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine , Durham, North Carolina 27710, United States
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108
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You X, Qin H, Ye M. Recent advances in methods for the analysis of protein o-glycosylation at proteome level. J Sep Sci 2017; 41:248-261. [PMID: 28988430 DOI: 10.1002/jssc.201700834] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/12/2022]
Abstract
O-Glycosylation, which refers to the glycosylation of the hydroxyl group of side chains of Serine/Threonine/Tyrosine residues, is one of the most common post-translational modifications. Compared with N-linked glycosylation, O-glycosylation is less explored because of its complex structure and relatively low abundance. Recently, O-glycosylation has drawn more and more attention for its various functions in many sophisticated biological processes. To obtain a deep understanding of O-glycosylation, many efforts have been devoted to develop effective strategies to analyze the two most abundant types of O-glycosylation, i.e. O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation. In this review, we summarize the proteomics workflows to analyze these two types of O-glycosylation. For the large-scale analysis of mucin-type glycosylation, the glycan simplification strategies including the ''SimpleCell'' technology were introduced. A variety of enrichment methods including lectin affinity chromatography, hydrophilic interaction chromatography, hydrazide chemistry, and chemoenzymatic method were introduced for the proteomics analysis of O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation.
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Affiliation(s)
- Xin You
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
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109
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Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Transl Res 2017; 189:30-50. [PMID: 28919341 PMCID: PMC5659875 DOI: 10.1016/j.trsl.2017.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/14/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The mammalian gut microbiota has been linked to host developmental, immunologic, and metabolic outcomes. This collection of trillions of microbes inhabits the gut and produces a myriad of metabolites, which are measurable in host circulation and contribute to the pathogenesis of human diseases. The link between endogenous metabolite availability and chromatin regulation is a well-established and active area of investigation; however, whether microbial metabolites can elicit similar effects is less understood. In this review, we focus on seminal and recent research that establishes chromatin regulatory roles for both endogenous and microbial metabolites. We also highlight key physiologic and disease settings where microbial metabolite-host chromatin interactions have been established and/or may be pertinent.
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Affiliation(s)
- Kimberly A Krautkramer
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis.
| | - Rashpal S Dhillon
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis; Morgridge Institute for Research, Madison, Wis
| | - Hannah V Carey
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, Wis
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110
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Hayakawa K, Hirosawa M, Tani R, Yoneda C, Tanaka S, Shiota K. H2A O-GlcNAcylation at serine 40 functions genomic protection in association with acetylated H2AZ or γH2AX. Epigenetics Chromatin 2017; 10:51. [PMID: 29084613 PMCID: PMC5663087 DOI: 10.1186/s13072-017-0157-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022] Open
Abstract
Background We have previously reported a novel O-GlcNAc modification at serine 40 (S40) of H2A (H2AS40Gc). S40-type H2A isoforms susceptible to O-GlcNAcylation are evolutionarily new and restricted to the viviparous animals; however, the biological function of H2AS40Gc is largely unknown. H2A isoforms are consisted of S40 and alanine 40 (A40) type and this residue on H2A is located in the L1 of the globular domain, which is also known as a variable portion that distinguishes between the canonical and non-canonical H2A variants. In this study, by considering the similarity between the S40-type H2A and histone H2A variants, we explored the function of H2AS40Gc in mouse embryonic stem cells (mESCs). Results We found several similarities between the S40-type H2A isoforms and histone H2A variants such H2AZ and H2AX. mRNA of S40-type H2A isoforms (H2A1 N and H2A3) had a poly(A) tail and was produced throughout the cell cycle in contrast to that of A40-type. Importantly, H2AS40Gc level increased owing to chemical-induced DNA damage, similar to phosphorylated H2AX (γH2AX) and acetylated H2AZ (AcH2AZ). H2AS40Gc was accumulated at the restricted area (± 1.5 kb) of DNA damage sites induced by CRISPR/CAS9 system in contrast to accumulation of γH2AX, which was widely scattered. Overexpression of the wild-type (WT) H2A3, but not the S40 to A40 mutation (S40A-mutant), protected the mESC genome against chemical-induced DNA damage. Furthermore, 3 h after the DNA damage treatment, the genome was almost recovered in WT mESCs, whereas the damage advanced further in the S40A-mutant mESCs, suggesting functions of H2AS40Gc in the DNA repair mechanism. Furthermore, the S40A mutant prevented the accumulation of the DNA repair apparatus such as DNA-PKcs and Rad51 at the damage site. Co-immunoprecipitation experiment in WT and S40A-mutant mESCs revealed that H2AS40Gc physiologically bound to AcH2AZ at the initial phase upon DNA damage, followed by binding with γH2AX during the DNA damage repair process. Conclusions These data suggest that H2AS40Gc functions to maintain genome integrity through the DNA repair mechanism in association with AcH2AZ and γH2AX. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0157-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Koji Hayakawa
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Mitsuko Hirosawa
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Ruiko Tani
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Chikako Yoneda
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Satoshi Tanaka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kunio Shiota
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, 113-8657, Japan. .,Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.
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111
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Zhang X, Liu J, Cao X. Metabolic control of T-cell immunity via epigenetic mechanisms. Cell Mol Immunol 2017; 15:203-205. [PMID: 29082922 DOI: 10.1038/cmi.2017.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Xiaomin Zhang
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Juan Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Xuetao Cao
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China.,Department of Immunology and Center for Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
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112
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Ma X, Li H, He Y, Hao J. The emerging link between O-GlcNAcylation and neurological disorders. Cell Mol Life Sci 2017; 74:3667-3686. [PMID: 28534084 PMCID: PMC11107615 DOI: 10.1007/s00018-017-2542-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 04/23/2017] [Accepted: 05/16/2017] [Indexed: 12/15/2022]
Abstract
O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) is involved in the regulation of many cellular cascades and neurological diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and stroke. In the brain, the expression of O-GlcNAcylation is notably heightened, as is that of O-linked N-acetylglucosaminyltransferase (OGT) and β-N-acetylglucosaminidase (OGA), the presence of which is prominent in many regions of neurological importance. Most importantly, O-GlcNAcylation is believed to contribute to the normal functioning of neurons; conversely, its dysregulation participates in the pathogenesis of neurological disorders. In neurodegenerative diseases, O-GlcNAcylation of the brain's key proteins, such as tau and amyloid-β, interacts with their phosphorylation, thereby triggering the formation of neurofibrillary tangles and amyloid plaques. An increase of O-GlcNAcylation by pharmacological intervention prevents neuronal loss. Additionally, O-GlcNAcylation is stress sensitive, and its elevation is cytoprotective. Increased O-GlcNAcylation ameliorated brain damage in victims of both trauma-hemorrhage and stroke. In this review, we summarize the current understanding of O-GlcNAcylation's physiological and pathological roles in the nervous system and provide a foundation for development of a therapeutic strategy for neurological disorders.
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Affiliation(s)
- Xiaofeng Ma
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - He Li
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yating He
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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113
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Abstract
The physiological identity of every cell is maintained by highly specific transcriptional networks that establish a coherent molecular program that is in tune with nutritional conditions. The regulation of cell-specific transcriptional networks is accomplished by an epigenetic program via chromatin-modifying enzymes, whose activity is directly dependent on metabolites such as acetyl-coenzyme A, S-adenosylmethionine, and NAD+, among others. Therefore, these nuclear activities are directly influenced by the nutritional status of the cell. In addition to nutritional availability, this highly collaborative program between epigenetic dynamics and metabolism is further interconnected with other environmental cues provided by the day-night cycles imposed by circadian rhythms. Herein, we review molecular pathways and their metabolites associated with epigenetic adaptations modulated by histone- and DNA-modifying enzymes and their responsiveness to the environment in the context of health and disease.
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114
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ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature 2017; 548:607-611. [PMID: 28767641 DOI: 10.1038/nature23671] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
Abstract
ATP-dependent chromatin remodellers regulate access to genetic information by controlling nucleosome positions in vivo. However, the mechanism by which remodellers discriminate between different nucleosome substrates is poorly understood. Many chromatin remodelling proteins possess conserved protein domains that interact with nucleosomal features. Here we used a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI family remodellers in response to a diverse set of nucleosome modifications. We show that accessory (non-ATPase) subunits of ISWI remodellers can distinguish between differentially modified nucleosomes, directing remodelling activity towards specific nucleosome substrates according to their modification state. Unexpectedly, we show that the nucleosome acidic patch is necessary for maximum activity of all ISWI remodellers evaluated. This dependence also extends to CHD and SWI/SNF family remodellers, suggesting that the acidic patch may be generally required for chromatin remodelling. Critically, remodelling activity can be regulated by modifications neighbouring the acidic patch, signifying that it may act as a tunable interaction hotspot for ATP-dependent chromatin remodellers and, by extension, many other chromatin effectors that engage this region of the nucleosome surface.
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115
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Potential coordination role between O-GlcNAcylation and epigenetics. Protein Cell 2017; 8:713-723. [PMID: 28488246 PMCID: PMC5636747 DOI: 10.1007/s13238-017-0416-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 11/25/2022] Open
Abstract
Dynamic changes of the post-translational O-GlcNAc modification (O-GlcNAcylation) are controlled by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and the glycoside hydrolase O-GlcNAcase (OGA) in cells. O-GlcNAcylation often occurs on serine (Ser) and threonine (Thr) residues of the specific substrate proteins via the addition of O-GlcNAc group by OGT. It has been known that O-GlcNAcylation is not only involved in many fundamental cellular processes, but also plays an important role in cancer development through various mechanisms. Recently, accumulating data reveal that O-GlcNAcylation at histones or non-histone proteins can lead to the start of the subsequent biological processes, suggesting that O-GlcNAcylation as ‘protein code’ or ‘histone code’ may provide recognition platforms or executive instructions for subsequent recruitment of proteins to carry out the specific functions. In this review, we summarize the interaction of O-GlcNAcylation and epigenetic changes, introduce recent research findings that link crosstalk between O-GlcNAcylation and epigenetic changes, and speculate on the potential coordination role of O-GlcNAcylation with epigenetic changes in intracellular biological processes.
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116
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O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview. Biochem Soc Trans 2017; 45:323-338. [PMID: 28408473 DOI: 10.1042/bst20160388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of histones and the dynamic DNA methylation cycle are finely regulated by a myriad of chromatin-binding factors and chromatin-modifying enzymes. Epigenetic modifications ensure local changes in the architecture of chromatin, thus controlling in fine the accessibility of the machinery of transcription, replication or DNA repair to the chromatin. Over the past decade, the nutrient-sensor enzyme O-GlcNAc transferase (OGT) has emerged as a modulator of chromatin remodeling. In mammals, OGT acts either directly through dynamic and reversible O-GlcNAcylation of histones and chromatin effectors, or in an indirect manner through its recruitment into chromatin-bound multiprotein complexes. In particular, there is an increasing amount of evidence of a cross-talk between OGT and the DNA dioxygenase ten-eleven translocation proteins that catalyze active DNA demethylation. Conversely, the stability of OGT itself can be controlled by the histone lysine-specific demethylase 2 (LSD2). Finally, a few studies have explored the role of O-GlcNAcase (OGA) in chromatin remodeling. In this review, we summarize the recent findings on the link between OGT, OGA and chromatin regulators in mammalian cellular models, and discuss their relevance in physiological and pathological conditions.
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117
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He D, Pengtao G, Ju Y, Jianhua L, He L, Guocai Z, Xichen Z. Differential Protein Expressions in Virus-Infected and Uninfected Trichomonas vaginalis. THE KOREAN JOURNAL OF PARASITOLOGY 2017; 55:121-128. [PMID: 28506033 PMCID: PMC5450954 DOI: 10.3347/kjp.2017.55.2.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 02/05/2017] [Accepted: 02/22/2017] [Indexed: 11/23/2022]
Abstract
Protozoan viruses may influence the function and pathogenicity of the protozoa. Trichomonas vaginalis is a parasitic protozoan that could contain a double stranded RNA (dsRNA) virus, T. vaginalis virus (TVV). However, there are few reports on the properties of the virus. To further determine variations in protein expression of T. vaginalis, we detected 2 strains of T. vaginalis; the virus-infected (V+) and uninfected (V−) isolates to examine differentially expressed proteins upon TVV infection. Using a stable isotope N-terminal labeling strategy (iTRAQ) on soluble fractions to analyze proteomes, we identified 293 proteins, of which 50 were altered in V+ compared with V− isolates. The results showed that the expression of 29 proteins was increased, and 21 proteins decreased in V+ isolates. These differentially expressed proteins can be classified into 4 categories: ribosomal proteins, metabolic enzymes, heat shock proteins, and putative uncharacterized proteins. Quantitative PCR was used to detect 4 metabolic processes proteins: glycogen phosphorylase, malate dehydrogenase, triosephosphate isomerase, and glucose-6-phosphate isomerase, which were differentially expressed in V+ and V− isolates. Our findings suggest that mRNA levels of these genes were consistent with protein expression levels. This study was the first which analyzed protein expression variations upon TVV infection. These observations will provide a basis for future studies concerning the possible roles of these proteins in host-parasite interactions.
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Affiliation(s)
- Ding He
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Gong Pengtao
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Yang Ju
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Li Jianhua
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Li He
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Zhang Guocai
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
| | - Zhang Xichen
- College of Veterinary Medicine, Jilin University, Changchun 130062, P. R. China
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118
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Wu D, Zhao L, Feng Z, Yu C, Ding J, Wang L, Wang F, Liu D, Zhu H, Xing F, Conaway JW, Conaway RC, Cai Y, Jin J. O-Linked N-acetylglucosamine transferase 1 regulates global histone H4 acetylation via stabilization of the nonspecific lethal protein NSL3. J Biol Chem 2017; 292:10014-10025. [PMID: 28450392 DOI: 10.1074/jbc.m117.781401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Indexed: 01/16/2023] Open
Abstract
The human males absent on the first (MOF)-containing histone acetyltransferase nonspecific lethal (NSL) complex comprises nine subunits including the O-linked N-acetylglucosamine (O-GlcNAc) transferase, isoform 1 (OGT1). However, whether the O-GlcNAc transferase activity of OGT1 controls histone acetyltransferase activity of the NSL complex and whether OGT1 physically interacts with the other NSL complex subunits remain unclear. Here, we demonstrate that OGT1 regulates the activity of the NSL complex by mainly acetylating histone H4 Lys-16, Lys-5, and Lys-8 via O-GlcNAcylation and stabilization of the NSL complex subunit NSL3. Knocking down or overexpressing OGT1 in human cells remarkably affected the global acetylation of histone H4 residues Lys-16, Lys-5, and Lys-8. Because OGT1 is a subunit of the NSL complex, we also investigated the function of OGT1 in this complex. Co-transfection/co-immunoprecipitation experiments combined with in vitro O-GlcNAc transferase assays confirmed that OGT1 specifically binds to and O-GlcNAcylates NSL3. In addition, wheat germ agglutinin affinity purification verified the occurrence of O-GlcNAc modification on NSL3 in cells. Moreover, O-GlcNAcylation of NSL3 by wild-type OGT1 (OGT1-WT) stabilized NSL3. This stabilization was lost after co-transfection of NSL3 with an OGT1 mutant, OGT1C964A, that lacks O-GlcNAc transferase activity. Furthermore, stabilization of NSL3 by OGT1-WT significantly increased the global acetylation levels of H4 Lys-5, Lys-8, and Lys-16 in cells. These results suggest that OGT1 regulates the activity of the NSL complex by stabilizing NSL3.
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Affiliation(s)
| | | | | | - Chao Yu
- From the School of Life Sciences
| | | | | | - Fei Wang
- From the School of Life Sciences
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | | | | | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Lawrence, Kansas 66045
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Lawrence, Kansas 66045
| | - Yong Cai
- From the School of Life Sciences, .,National Engineering Laboratory for AIDS Vaccine, and.,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun 130012, China
| | - Jingji Jin
- From the School of Life Sciences, .,National Engineering Laboratory for AIDS Vaccine, and.,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun 130012, China
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119
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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: 1.3] [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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120
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Zhang P, Torres K, Liu X, Liu CG, Pollock RE. An Overview of Chromatin-Regulating Proteins in Cells. Curr Protein Pept Sci 2017; 17:401-10. [PMID: 26796306 DOI: 10.2174/1389203717666160122120310] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 12/25/2015] [Accepted: 12/30/2015] [Indexed: 12/13/2022]
Abstract
In eukaryotic cells, gene expressions on chromosome DNA are orchestrated by a dynamic chromosome structure state that is largely controlled by chromatin-regulating proteins, which regulate chromatin structures, release DNA from the nucleosome, and activate or suppress gene expression by modifying nucleosome histones or mobilizing DNA-histone structure. The two classes of chromatinregulating proteins are 1) enzymes that modify histones through methylation, acetylation, phosphorylation, adenosine diphosphate-ribosylation, glycosylation, sumoylation, or ubiquitylation and 2) enzymes that remodel DNA-histone structure with energy from ATP hydrolysis. Chromatin-regulating proteins, which modulate DNA-histone interaction, change chromatin conformation, and increase or decrease the binding of functional DNA-regulating protein complexes, have major functions in nuclear processes, including gene transcription and DNA replication, repair, and recombination. This review provides a general overview of chromatin-regulating proteins, including their classification, molecular functions, and interactions with the nucleosome in eukaryotic cells.
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Affiliation(s)
- Pingyu Zhang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
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121
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Reddy BA, Jeronimo C, Robert F. Recent Perspectives on the Roles of Histone Chaperones in Transcription Regulation. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0049-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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122
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Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches. Oncogene 2017; 36:3359-3374. [PMID: 28092669 PMCID: PMC5485177 DOI: 10.1038/onc.2016.485] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023]
Abstract
Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer.
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123
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Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
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124
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Igarashi M, Sakamoto K, Nagaoka I. Effect of glucosamine on expression of type II collagen, matrix metalloproteinase and sirtuin genes in a human chondrocyte cell line. Int J Mol Med 2016; 39:472-478. [PMID: 28035358 DOI: 10.3892/ijmm.2016.2842] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 12/15/2016] [Indexed: 11/06/2022] Open
Abstract
Glucosamine (GlcN) has been widely used to treat osteoarthritis (OA) in humans. However, the effects of GlcN on genes related to cartilage metabolism are still unknown. In the present study, to elucidate the chondroprotective action of GlcN on OA, we examined the effects of GlcN (0.1-10 mM) on the expression of the sirtuin (SIRT) genes as well as type II collagen and matrix metalloproteinases (MMPs) using a human chondrocyte cell line SW 1353. SW 1353 cells were incubated in the absence or presence of GlcN. RT-PCR analyses revealed that GlcN markedly increased the mRNA expression of type II collagen (COL2A1). By contrast, the levels of MMP-1 and MMP-9 mRNA were only slightly increased by GlcN. Furthermore, western blot analyses revealed that GlcN significantly increased the protein level of COL2A1. Importantly, GlcN enhanced the mRNA expression and protein level of SIRT1, an upstream-regulating gene of COL2A1. Moreover, a SIRT1 inhibitor suppressed GlcN-induced COL2A1 gene expression. Together these observations suggest that GlcN enhances the mRNA expression and protein level of SIRT1 and its downstream gene COL2A1 in chondrocytes, thereby possibly exhibiting chondroprotective action on OA.
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Affiliation(s)
- Mamoru Igarashi
- Department of Host Defense and Biochemical Research, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Koji Sakamoto
- Department of Host Defense and Biochemical Research, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Isao Nagaoka
- Department of Host Defense and Biochemical Research, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
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125
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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126
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Lu H, Li G, Zhou C, Jin W, Qian X, Wang Z, Pan H, Jin H, Wang X. Regulation and role of post-translational modifications of enhancer of zeste homologue 2 in cancer development. Am J Cancer Res 2016; 6:2737-2754. [PMID: 28042497 PMCID: PMC5199751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023] Open
Abstract
Post-translational modifications (PTMs) are critical molecular events which alter protein conformation after their synthesis and diversity protein properties by modulating their stability, localization, interacting partners or the activity of their substrates, consequently exerting pivotal roles in regulating the functions of many important eukaryotic proteins. It has been well acknowledged that PTMs are of great importance in a broad range of biological processes such as gene regulation, cell proliferation, differentiation and apoptosis, tissue development, diseases, tumor progression and drug resistance. As the core and contributing catalytic subunit of Polycomb repressive complex 2(PRC2), Enhancer of zeste homolog 2 (EZH2) is a master epigenetic regulator, often serving as a highly conserved histone methyltransferase (HMTase) to induce histone H3 lysine 27 trimethylation (H3K27me3) and repress gene transcription and expression. Dysregulated EZH2 expression is frequently associated with cancer development and poor prognosis in a wide variety of cancers. Considered its essential role in carcinogenesis, EZH2 is a potential candidate for cancer targeted therapy. Remarkably, mounting evidence highlights that EZH2 expression, activity and stability can be regulated by PTMs including phosphorylation, acetylation, ubiquitination, sumoylation and GlcNAcylation aside from its well-validated modifications in transcriptional and post-transcriptional levels. However, the precise regulatory mechanisms underlying EZH2 PTMs and whether other types of PTMs orchestrate in EZH2 remain largely unclear. In this review, we summarize current advances in the understanding of EZH2 regulation by PTMs and their associated biological functions during tumorigenesis.
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Affiliation(s)
- Haiqi Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Guangliang Li
- Department of Medical Oncology, Zhejiang Cancer HospitalHangzhou, Zhejiang, China
| | - Chenyi Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Wei Jin
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Xiaoling Qian
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Zhuo Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
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127
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Abstract
The O-linked N-acetylglucosamine (O-GlcNAc) post-translational modification (O-GlcNAcylation) is the dynamic and reversible attachment of N-acetylglucosamine to serine and threonine residues of nucleocytoplasmic target proteins. It is abundant in metazoa, involving hundreds of proteins linked to a plethora of biological functions with implications in human diseases. The process is catalysed by two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) that add and remove sugar moieties respectively. OGT knockout is embryonic lethal in a range of animal models, hampering the study of the biological role of O-GlcNAc and the dissection of catalytic compared with non-catalytic roles of OGT. Therefore, selective and potent chemical tools are necessary to inhibit OGT activity in the context of biological systems. The present review focuses on the available OGT inhibitors and summarizes advantages, limitations and future challenges.
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128
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Mariappa D, Zheng X, Schimpl M, Raimi O, Ferenbach AT, Müller HAJ, van Aalten DMF. Dual functionality of O-GlcNAc transferase is required for Drosophila development. Open Biol 2016; 5:150234. [PMID: 26674417 PMCID: PMC4703063 DOI: 10.1098/rsob.150234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Post-translational modification of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc) catalysed by O-GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein-protein interactions. Drosophila OGT (DmOGT) is encoded by super sex combs (sxc), mutants of which are pupal lethal. However, it is not clear if this phenotype is caused by reduction of O-GlcNAcylation. Here we use a genetic approach to demonstrate that post-pupal Drosophila development can proceed with negligible OGT catalysis, while early embryonic development is OGT activity-dependent. Structural and enzymatic comparison between human OGT (hOGT) and DmOGT informed the rational design of DmOGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements sxc pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of Hox genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.
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Affiliation(s)
- Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Xiaowei Zheng
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Marianne Schimpl
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Olawale Raimi
- Division of Molecular Microbiology, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - H-Arno J Müller
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK Division of Molecular Microbiology, University of Dundee, Dundee, UK
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129
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Effects of heterologous expression of human cyclic nucleotide phosphodiesterase 3A (hPDE3A) on redox regulation in yeast. Biochem J 2016; 473:4205-4225. [PMID: 27647936 DOI: 10.1042/bcj20160572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/07/2016] [Accepted: 09/19/2016] [Indexed: 01/11/2023]
Abstract
Oxidative stress plays a pivotal role in pathogenesis of cardiovascular diseases and diabetes; however, the roles of protein kinase A (PKA) and human phosphodiesterase 3A (hPDE3A) remain unknown. Here, we show that yeast expressing wild-type (WT) hPDE3A or K13R hPDE3A (putative ubiquitinylation site mutant) exhibited resistance or sensitivity to exogenous hydrogen peroxide (H2O2), respectively. H2O2-stimulated ROS production was markedly increased in yeast expressing K13R hPDE3A (Oxidative stress Sensitive 1, OxiS1), compared with yeast expressing WT hPDE3A (Oxidative stress Resistant 1, OxiR1). In OxiR1, YAP1 and YAP1-dependent antioxidant genes were up-regulated, accompanied by a reduction in thioredoxin peroxidase. In OxiS1, expression of YAP1 and YAP1-dependent genes was impaired, and the thioredoxin system malfunctioned. H2O2 increased cyclic adenosine monophosphate (cAMP)-hydrolyzing activity of WT hPDE3A, but not K13R hPDE3A, through PKA-dependent phosphorylation of hPDE3A, which was correlated with its ubiquitinylation. The changes in antioxidant gene expression did not directly correlate with differences in cAMP-PKA signaling. Despite differences in their capacities to hydrolyze cAMP, total cAMP levels among OxiR1, OxiS1, and mock were similar; PKA activity, however, was lower in OxiS1 than in OxiR1 or mock. During exposure to H2O2, however, Sch9p activity, a target of Rapamycin complex 1-regulated Rps6 kinase and negative-regulator of PKA, was rapidly reduced in OxiR1, and Tpk1p, a PKA catalytic subunit, was diffusely spread throughout the cytosol, with PKA activation. In OxiS1, Sch9p activity was unchanged during exposure to H2O2, consistent with reduced activation of PKA. These results suggest that, during oxidative stress, TOR-Sch9 signaling might regulate PKA activity, and that post-translational modifications of hPDE3A are critical in its regulation of cellular recovery from oxidative stress.
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130
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Novel O-GlcNAcylation on Ser(40) of canonical H2A isoforms specific to viviparity. Sci Rep 2016; 6:31785. [PMID: 27615797 PMCID: PMC5018834 DOI: 10.1038/srep31785] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/26/2016] [Indexed: 11/23/2022] Open
Abstract
We report here newly discovered O-linked-N-acetylglucosamine (O-GlcNAc) modification of histone H2A at Ser40 (H2AS40Gc). The mouse genome contains 18 H2A isoforms, of which 13 have Ser40 and the other five have Ala40. The combination of production of monoclonal antibody and mass spectrometric analyses with reverse-phase (RP)-high performance liquid chromatography (HPLC) fractionation indicated that the O-GlcNAcylation is specific to the Ser40 isoforms. The H2AS40Gc site is in the L1 loop structure where two H2A molecules interact in the nucleosome. Targets of H2AS40Gc are distributed genome-wide and are dramatically changed during the process of differentiation in mouse trophoblast stem cells. In addition to the mouse, H2AS40Gc was also detected in humans, macaques and cows, whereas non-mammalian species possessing only the Ala40 isoforms, such as silkworms, zebrafish and Xenopus showed no signal. Genome database surveys revealed that Ser40 isoforms of H2A emerged in Marsupialia and persisted thereafter in mammals. We propose that the emergence of H2A Ser40 and its O-GlcNAcylation linked a genetic event to genome-wide epigenetic events that correlate with the evolution of placental animals.
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131
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Duan Y, Huo D, Gao J, Wu H, Ye Z, Liu Z, Zhang K, Shan L, Zhou X, Wang Y, Su D, Ding X, Shi L, Wang Y, Shang Y, Xuan C. Ubiquitin ligase RNF20/40 facilitates spindle assembly and promotes breast carcinogenesis through stabilizing motor protein Eg5. Nat Commun 2016; 7:12648. [PMID: 27557628 PMCID: PMC5007379 DOI: 10.1038/ncomms12648] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 07/19/2016] [Indexed: 12/30/2022] Open
Abstract
Whether transcriptional regulators are functionally involved in mitosis is a fundamental question in cell biology. Here we report that the RNF20/40 complex, a major ubiquitin ligase catalysing histone H2B monoubiquitination, interacts with the motor protein Eg5 during mitosis and participates in spindle assembly. We show that the RNF20/40 complex monoubiquitinates and stabilizes Eg5. Loss of RNF20/40 results in spindle assembly defects, cell cycle arrest and apoptosis. Consistently, depletion of either RNF20/40 or Eg5 suppresses breast cancer in vivo. Significantly, RNF20/40 and Eg5 are concurrently upregulated in human breast carcinomas and high Eg5 expression is associated with poorer overall survival of patients with luminal A, or B, breast cancer. Our study uncovers an important spindle assembly role of the RNF20/40 complex, and implicates the RNF20/40-Eg5 axis in breast carcinogenesis, supporting the pursuit of these proteins as potential targets for breast cancer therapeutic interventions. Eg5 has a role in spindle assembly and has been associated with tumorigenesis but it is not clear how its activity is regulated. Here, the authors show that the E3 ligase RNF20/40 regulates mitotic spindle assembly by regulating the stability of Eg5 through mono-ubiquitination of K745.
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Affiliation(s)
- Yang Duan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Dawei Huo
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Jie Gao
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Heng Wu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumour Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zheng Ye
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Zhe Liu
- Department of Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Xing Zhou
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Dongxue Su
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Ding
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yan Wang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
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132
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Sato H, Wheat JC, Steidl U, Ito K. DNMT3A and TET2 in the Pre-Leukemic Phase of Hematopoietic Disorders. Front Oncol 2016; 6:187. [PMID: 27597933 PMCID: PMC4992944 DOI: 10.3389/fonc.2016.00187] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/05/2016] [Indexed: 12/19/2022] Open
Abstract
In recent years, advances in next-generation sequencing (NGS) technology have provided the opportunity to detect putative genetic drivers of disease, particularly cancers, with very high sensitivity. This knowledge has substantially improved our understanding of tumor pathogenesis. In hematological malignancies such as acute myeloid leukemia and myelodysplastic syndromes, pioneering work combining multi-parameter flow cytometry and targeted resequencing in leukemia have clearly shown that different classes of mutations appear to be acquired in particular sequences along the hematopoietic differentiation hierarchy. Moreover, as these mutations can be found in “normal” cells recovered during remission and can be detected at relapse, there is strong evidence for the existence of “pre-leukemic” stem cells (pre-LSC). These cells, while phenotypically normal by flow cytometry, morphology, and functional studies, are speculated to be molecularly poised to transform owing to a limited number of predisposing mutations. Identifying these “pre-leukemic” mutations and how they propagate a pre-malignant state has important implications for understanding the etiology of these disorders and for the development of novel therapeutics. NGS studies have found a substantial enrichment for mutations in epigenetic/chromatin remodeling regulators in pre-LSC, and elegant genetic models have confirmed that these mutations can predispose to a variety of hematological malignancies. In this review, we will discuss the current understanding of pre-leukemic biology in myeloid malignancies, and how mutations in two key epigenetic regulators, DNMT3A and TET2, may contribute to disease pathogenesis.
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Affiliation(s)
- Hanae Sato
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Justin C Wheat
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ulrich Steidl
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA; Einstein Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
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133
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Murawska M, Ladurner AG. CENPs and Sweet Nucleosomes Face the FACT. Trends Biochem Sci 2016; 41:736-738. [PMID: 27499233 DOI: 10.1016/j.tibs.2016.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/20/2016] [Indexed: 11/29/2022]
Abstract
Chaperones mediate vital interactions between histones and DNA during chromatin assembly and reorganization. Two recent studies reveal novel substrates for the essential and conserved histone chaperone FAcilitates Chromatin Transcription (FACT). Prendergast et al. show that FACT helps deposit important histone-fold proteins on centromeres. Raj et al. find that FACT preferentially binds O-GlcNAcylated nucleosomes, suggesting that FACT may contribute to nutrient-regulated cellular programs.
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Affiliation(s)
- Magdalena Murawska
- Biomedical Center, Physiological Chemistry, LMU Munich, Großhaderner Street 9, 82152 Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center, Physiological Chemistry, LMU Munich, Großhaderner Street 9, 82152 Planegg-Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany.
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134
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Abstract
High-risk human papillomaviruses (HPVs) are causative agents of anogenital cancers and a fraction of head and neck cancers. The mechanisms involved in the progression of HPV neoplasias to cancers remain largely unknown. Here, we report that O-linked GlcNAcylation (O-GlcNAc) and O-GlcNAc transferase (OGT) were markedly increased in HPV-caused cervical neoplasms relative to normal cervix, whereas O-GlcNAcase (OGA) levels were not altered. Transduction of HPV16 oncogene E6 or E6/E7 into mouse embryonic fibroblasts (MEFs) up-regulated OGT mRNA and protein, elevated the level of O-GlcNAc, and promoted cell proliferation while reducing cellular senescence. Conversely, in HPV-18-transformed HeLa cervical carcinoma cells, inhibition of O-GlcNAc with a low concentration of a chemical inhibitor impaired the transformed phenotypes in vitro. We showed that E6 elevated c-MYC via increased protein stability attributable to O-GlcNAcylation on Thr58. Reduction of HPV-mediated cell viability by a high concentration of O-GlcNAc inhibitor was partially rescued by elevated c-MYC. Finally, knockdown of OGT or O-GlcNAc inhibition in HeLa cells or in TC-1 cells, a mouse cell line transformed by HPV16 E6/E7 and activated K-RAS, reduced c-MYC and suppressed tumorigenesis and metastasis. Thus, we have uncovered a mechanism for HPV oncoprotein-mediated transformation. These findings may eventually aid in the development of effective therapeutics for HPV-associated malignancies by targeting aberrant O-GlcNAc.
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135
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Raj R, Lercher L, Mohammed S, Davis BG. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex. Angew Chem Int Ed Engl 2016; 55:8918-22. [PMID: 27272618 PMCID: PMC5111754 DOI: 10.1002/anie.201603106] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 12/28/2022]
Abstract
Transcriptional regulation can be established by various post-translational modifications (PTMs) on histone proteins in the nucleosome and by nucleobase modifications on chromosomal DNA. Functional consequences of histone O-GlcNAcylation (O-GlcNAc=O-linked β-N-acetylglucosamine) are largely unexplored. Herein, we generate homogeneously GlcNAcylated histones and nucleosomes by chemical post-translational modification. Mass-spectrometry-based quantitative interaction proteomics reveals a direct interaction between GlcNAcylated nucleosomes and the "facilitates chromatin transcription" (FACT) complex. Preferential binding of FACT to GlcNAcylated nucleosomes may point towards O-GlcNAcylation as one of the triggers for FACT-driven transcriptional control.
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Affiliation(s)
- Ritu Raj
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lukas Lercher
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.
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136
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Raj R, Lercher L, Mohammed S, Davis BG. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ritu Raj
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Lukas Lercher
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Shabaz Mohammed
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Benjamin G. Davis
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
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137
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Zhang Z, Costa FC, Tan EP, Bushue N, DiTacchio L, Costello CE, McComb ME, Whelan SA, Peterson KR, Slawson C. O-Linked N-Acetylglucosamine (O-GlcNAc) Transferase and O-GlcNAcase Interact with Mi2β Protein at the Aγ-Globin Promoter. J Biol Chem 2016; 291:15628-40. [PMID: 27231347 DOI: 10.1074/jbc.m116.721928] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 12/23/2022] Open
Abstract
One mode of γ-globin gene silencing involves a GATA-1·FOG-1·Mi2β repressor complex that binds to the -566 GATA site relative to the (A)γ-globin gene cap site. However, the mechanism of how this repressor complex is assembled at the -566 GATA site is unknown. In this study, we demonstrate that the O-linked N-acetylglucosamine (O-GlcNAc) processing enzymes, O-GlcNAc-transferase (OGT) and O-GlcNAcase (OGA), interact with the (A)γ-globin promoter at the -566 GATA repressor site; however, mutation of the GATA site to GAGA significantly reduces OGT and OGA promoter interactions in β-globin locus yeast artificial chromosome (β-YAC) bone marrow cells. When WT β-YAC bone marrow cells are treated with the OGA inhibitor Thiamet-G, the occupancy of OGT, OGA, and Mi2β at the (A)γ-globin promoter is increased. In addition, OGT and Mi2β recruitment is increased at the (A)γ-globin promoter when γ-globin becomes repressed in postconception day E18 human β-YAC transgenic mouse fetal liver. Furthermore, we show that Mi2β is modified with O-GlcNAc, and both OGT and OGA interact with Mi2β, GATA-1, and FOG-1. Taken together, our data suggest that O-GlcNAcylation is a novel mechanism of γ-globin gene regulation mediated by modulating the assembly of the GATA-1·FOG-1·Mi2β repressor complex at the -566 GATA motif within the promoter.
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Affiliation(s)
- Zhen Zhang
- From the Department of Biochemistry and Molecular Biology
| | | | - Ee Phie Tan
- From the Department of Biochemistry and Molecular Biology
| | - Nathan Bushue
- From the Department of Biochemistry and Molecular Biology
| | | | - Catherine E Costello
- Department of Biochemistry and Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, and
| | - Mark E McComb
- Department of Biochemistry and Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, and
| | - Stephen A Whelan
- Department of Biochemistry and Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, and
| | - Kenneth R Peterson
- From the Department of Biochemistry and Molecular Biology, Anatomy and Cell Biology, and Cancer Center, Institute for Reproductive Health and Regenerative Medicine, and
| | - Chad Slawson
- From the Department of Biochemistry and Molecular Biology, Cancer Center, Institute for Reproductive Health and Regenerative Medicine, and Alzheimer's Disease Center, University of Kansas Medical Center, Kansas City, Kansas 66160,
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138
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Gagnon J, Daou S, Zamorano N, Iannantuono NVG, Hammond-Martel I, Mashtalir N, Bonneil E, Wurtele H, Thibault P, Affar EB. Undetectable histone O-GlcNAcylation in mammalian cells. Epigenetics 2016; 10:677-91. [PMID: 26075789 DOI: 10.1080/15592294.2015.1060387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
O-GlcNAcylation is a posttranslational modification catalyzed by the O-Linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) and reversed by O-GlcNAcase (OGA). Numerous transcriptional regulators, including chromatin modifying enzymes, transcription factors, and co-factors, are targeted by O-GlcNAcylation, indicating that this modification is central for chromatin-associated processes. Recently, OGT-mediated O-GlcNAcylation was reported to be a novel histone modification, suggesting a potential role in directly coordinating chromatin structure and function. In contrast, using multiple biochemical approaches, we report here that histone O-GlcNAcylation is undetectable in mammalian cells. Conversely, O-GlcNAcylation of the transcription regulators Host Cell Factor-1 (HCF-1) and Ten-Eleven Translocation protein 2 (TET2) could be readily observed. Our study raises questions on the occurrence and abundance of O-GlcNAcylation as a histone modification in mammalian cells and reveals technical complications regarding the detection of genuine protein O-GlcNAcylation. Therefore, the identification of the specific contexts in which histone O-GlcNAcylation might occur is still to be established.
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Key Words
- Chromatin
- Epigenetics
- H2B K120ub, Histone H2B lysine 120 monoubiquitination
- H2B S112 O-GlcNAc, Histone H2B serine 112 O-GlcNAc
- HCF-1
- HCF-1, Host Cell Factor-1
- Histone
- O-GlcNAc
- O-GlcNAc, O-Linked N-acetylglucosamine
- O-GlcNAcylation
- OGA, O-GlcNAcase
- OGT
- OGT, O-Linked N-acetylglucosamine transferase
- PUGNAc, O-(2-acetamido-2-deoxyglucopyranosylidene) amino N-phenylcarbamate
- Polycomb
- TET2
- TET2, Ten-Eleven Translocation protein 2
- UDP-GlcNAc, Uridine Diphosphate N-Acetylglucosamine
- WGA, Wheat Germ Agglutinin.
- posttranslational modification
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Affiliation(s)
- Jessica Gagnon
- a Maisonneuve-Rosemont Hospital Research Center and Department of Medicine; University of Montréal ; Montréal, Québec , Canada
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139
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Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Mol Cell Proteomics 2016; 15:2462-75. [PMID: 27114449 DOI: 10.1074/mcp.o115.049627] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 12/28/2022] Open
Abstract
Over the past decades, protein O-GlcNAcylation has been found to play a fundamental role in cell cycle control, metabolism, transcriptional regulation, and cellular signaling. Nevertheless, quantitative approaches to determine in vivo GlcNAc dynamics at a large-scale are still not readily available. Here, we have developed an approach to isotopically label O-GlcNAc modifications on proteins by producing (13)C-labeled UDP-GlcNAc from (13)C6-glucose via the hexosamine biosynthetic pathway. This metabolic labeling was combined with quantitative mass spectrometry-based proteomics to determine protein O-GlcNAcylation turnover rates. First, an efficient enrichment method for O-GlcNAc peptides was developed with the use of phenylboronic acid solid-phase extraction and anhydrous DMSO. The near stoichiometry reaction between the diol of GlcNAc and boronic acid dramatically improved the enrichment efficiency. Additionally, our kinetic model for turnover rates integrates both metabolomic and proteomic data, which increase the accuracy of the turnover rate estimation. Other advantages of this metabolic labeling method include in vivo application, direct labeling of the O-GlcNAc sites and higher confidence for site identification. Concentrating only on nuclear localized GlcNAc modified proteins, we are able to identify 105 O-GlcNAc peptides on 42 proteins and determine turnover rates of 20 O-GlcNAc peptides from 14 proteins extracted from HeLa nuclei. In general, we found O-GlcNAcylation turnover rates are slower than those published for phosphorylation or acetylation. Nevertheless, the rates widely varied depending on both the protein and the residue modified. We believe this methodology can be broadly applied to reveal turnovers/dynamics of protein O-GlcNAcylation from different biological states and will provide more information on the significance of O-GlcNAcylation, enabling us to study the temporal dynamics of this critical modification for the first time.
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Affiliation(s)
- Xiaoshi Wang
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Zuo-Fei Yuan
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jing Fan
- §Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715
| | - Kelly R Karch
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Lauren E Ball
- ¶Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - John M Denu
- §Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715
| | - Benjamin A Garcia
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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140
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Zhu G, Tao T, Zhang D, Liu X, Qiu H, Han L, Xu Z, Xiao Y, Cheng C, Shen A. O-GlcNAcylation of histone deacetylases 1 in hepatocellular carcinoma promotes cancer progression. Glycobiology 2016; 26:820-833. [DOI: 10.1093/glycob/cww025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/22/2016] [Indexed: 12/12/2022] Open
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141
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142
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Jiang K, Bai B, Ta Y, Zhang T, Xiao Z, Wang PG, Zhang L. O-GlcNAc regulates NEDD4-1 stability via caspase-mediated pathway. Biochem Biophys Res Commun 2016; 471:539-44. [PMID: 26876577 DOI: 10.1016/j.bbrc.2016.02.037] [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] [Received: 02/02/2016] [Accepted: 02/10/2016] [Indexed: 01/13/2023]
Abstract
O-GlcNAc modification of cytosolic and nuclear proteins regulates essential cellular processes such as stress responses, transcription, translation, and protein degradation. Emerging evidence indicates O-GlcNAcylation has a dynamic interplay with ubiquitination in cellular regulation. Here, we report that O-GlcNAc indirectly targets a vital E3 ubiquitin ligase enzyme of NEDD4-1. The protein level of NEDD4-1 is accordingly decreased following an increase of overall O-GlcNAc level upon PUGNAc or glucosamine stimulation. O-GlcNAc transferase (OGT) knockdown, overexpression and mutation results confirm that the stability of NEDD4-1 is negatively regulated by cellular O-GlcNAc. Moreover, the NEDD4-1 degradation induced by PUGNAc or GlcN is significantly inhibited by the caspase inhibitor. Our study reveals a regulation mechanism of NEDD4-1 stability by O-GlcNAcylation.
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Affiliation(s)
- Kuan Jiang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Bingyang Bai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Yajie Ta
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Tingling Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Zikang Xiao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Peng George Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China.
| | - Lianwen Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China.
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143
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Hypoxia, Epithelial-Mesenchymal Transition, and TET-Mediated Epigenetic Changes. J Clin Med 2016; 5:jcm5020024. [PMID: 26861406 PMCID: PMC4773780 DOI: 10.3390/jcm5020024] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/15/2016] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Tumor hypoxia is a pathophysiologic outcome of disrupted microcirculation with inadequate supply of oxygen, leading to enhanced proliferation, epithelial-mesenchymal transition (EMT), metastasis, and chemo-resistance. Epigenetic changes induced by hypoxia are well documented, and they lead to tumor progression. Recent advances show that DNA demethylation mediated by the Ten-eleven translocation (TET) proteins induces major epigenetic changes and controls key steps of cancer development. TET enzymes serve as 5mC (5-methylcytosine)-specific dioxygenases and cause DNA demethylation. Hypoxia activates the expression of TET1, which also serves as a co-activator of HIF-1α transcriptional regulation to modulate HIF-1α downstream target genes and promote epithelial-mesenchymal transition. As HIF is a negative prognostic factor for tumor progression, hypoxia-activated prodrugs (HAPs) may provide a favorable therapeutic approach to lessen hypoxia-induced malignancy.
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144
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Fahrenkrog B. Histone modifications as regulators of life and death in Saccharomyces cerevisiae. MICROBIAL CELL 2015; 3:1-13. [PMID: 28357312 PMCID: PMC5354586 DOI: 10.15698/mic2016.01.472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Apoptosis or programmed cell death is an integrated, genetically controlled
suicide program that not only regulates tissue homeostasis of multicellular
organisms, but also the fate of damaged and aged cells of lower eukaryotes, such
as the yeast Saccharomyces cerevisiae. Recent years have
revealed key apoptosis regulatory proteins in yeast that play similar roles in
mammalian cells. Apoptosis is a process largely defined by characteristic
structural rearrangements in the dying cell that include chromatin condensation
and DNA fragmentation. The mechanism by which chromosomes restructure during
apoptosis is still poorly understood, but it is becoming increasingly clear that
altered epigenetic histone modifications are fundamental parameters that
influence the chromatin state and the nuclear rearrangements within apoptotic
cells. The present review will highlight recent work on the epigenetic
regulation of programmed cell death in budding yeast.
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Affiliation(s)
- Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Rue Profs. Jeener et Brachet 12; 6041 Charleroi, Belgium
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145
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Mitrousis N, Tropepe V, Hermanson O. Post-Translational Modifications of Histones in Vertebrate Neurogenesis. Front Neurosci 2015; 9:483. [PMID: 26733796 PMCID: PMC4689847 DOI: 10.3389/fnins.2015.00483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/04/2015] [Indexed: 11/13/2022] Open
Abstract
The process of neurogenesis, through which the entire nervous system of an organism is formed, has attracted immense scientific attention for decades. How can a single neural stem cell give rise to astrocytes, oligodendrocytes, and neurons? Furthermore, how is a neuron led to choose between the hundreds of different neuronal subtypes that the vertebrate CNS contains? Traditionally, niche signals and transcription factors have been on the spotlight. Recent research is increasingly demonstrating that the answer may partially lie in epigenetic regulation of gene expression. In this article, we comprehensively review the role of post-translational histone modifications in neurogenesis in both the embryonic and adult CNS.
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Affiliation(s)
- Nikolaos Mitrousis
- Institute of Biomaterials and Biomedical Engineering, University of Toronto Toronto, ON, Canada
| | - Vincent Tropepe
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto Toronto, ON, Canada
| | - Ola Hermanson
- Department of Neuroscience, Karolinska Institutet Stockholm, Sweden
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146
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Ding X, Jiang W, Zhou P, Liu L, Wan X, Yuan X, Wang X, Chen M, Chen J, Yang J, Kong C, Li B, Peng C, Wong CCL, Hou F, Zhang Y. Mixed Lineage Leukemia 5 (MLL5) Protein Stability Is Cooperatively Regulated by O-GlcNac Transferase (OGT) and Ubiquitin Specific Protease 7 (USP7). PLoS One 2015; 10:e0145023. [PMID: 26678539 PMCID: PMC4683056 DOI: 10.1371/journal.pone.0145023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/28/2015] [Indexed: 02/07/2023] Open
Abstract
Mixed lineage leukemia 5 (MLL5) protein is a trithorax family histone 3 lysine 4 (H3K4) methyltransferase that regulates diverse biological processes, including cell cycle progression, hematopoiesis and cancer. The mechanisms by which MLL5 protein stability is regulated have remained unclear to date. Here, we showed that MLL5 protein stability is cooperatively regulated by O-GlcNAc transferase (OGT) and ubiquitin-specific protease 7 (USP7). Depletion of OGT in cells led to a decrease in the MLL5 protein level through ubiquitin/proteasome-dependent proteolytic degradation, whereas ectopic expression of OGT protein suppressed MLL5 ubiquitylation. We further identified deubiquitinase USP7 as a novel MLL5-associated protein using mass spectrometry. USP7 stabilized the MLL5 protein through direct binding and deubiquitylation. Loss of USP7 induced degradation of MLL5 protein. Conversely, overexpression of USP7, but not a catalytically inactive USP7 mutant, led to decreased ubiquitylation and increased MLL5 stability. Co-immunoprecipitation and co-immunostaining assays revealed that MLL5, OGT and USP7 interact with each other to form a stable ternary complex that is predominantly located in the nucleus. In addition, upregulation of MLL5 expression was correlated with increased expression of OGT and USP7 in human primary cervical adenocarcinomas. Our results collectively reveal a novel molecular mechanism underlying regulation of MLL5 protein stability and provide new insights into the functional interplay among O-GlcNAc transferase, deubiquitinase and histone methyltransferase.
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Affiliation(s)
- Xiaodan Ding
- Department of Immunology, Nanjing Medical University, Jiangsu, China
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Wei Jiang
- Shanghai Red House Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- * E-mail: (WJ); (YZ)
| | - Peipei Zhou
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Lulu Liu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Institute of Biology and Medical Sciences, Soochow University, Jiangsu, China
| | - Xiaoling Wan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xiujie Yuan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xizi Wang
- College of life science, Sun Yet-Sen University, Guangzhou, China
| | - Miao Chen
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jun Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jing Yang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chao Kong
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Bin Li
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chao Peng
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Catherine C. L. Wong
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fajian Hou
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (WJ); (YZ)
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147
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Abstract
Dynamic cycling of N-Acetylglucosamine (GlcNAc) on serine and threonine residues (O-GlcNAcylation) is an essential process in all eukaryotic cells except yeast, including Saccharomyces cerevisiae and Schizosaccharomyces pombe. O-GlcNAcylation modulates signaling and cellular processes in an intricate interplay with protein phosphorylation and serves as a key sensor of nutrients by linking the hexosamine biosynthetic pathway to cellular signaling. A longstanding conundrum has been how yeast survives without O-GlcNAcylation in light of its similar phosphorylation signaling system. We previously developed a sensitive lectin enrichment and mass spectrometry workflow for identification of the human O-linked mannose (O-Man) glycoproteome and used this to identify a pleothora of O-Man glycoproteins in human cell lines including the large family of cadherins and protocadherins. Here, we applied the workflow to yeast with the aim to characterize the yeast O-Man glycoproteome, and in doing so, we discovered hitherto unknown O-Man glycosites on nuclear, cytoplasmic, and mitochondrial proteins in S. cerevisiae and S. pombe. Such O-Man glycoproteins were not found in our analysis of human cell lines. However, the type of yeast O-Man nucleocytoplasmic proteins and the localization of identified O-Man residues mirror that of the O-GlcNAc glycoproteome found in other eukaryotic cells, indicating that the two different types of O-glycosylations serve the same important biological functions. The discovery opens for exploration of the enzymatic machinery that is predicted to regulate the nucleocytoplasmic O-Man glycosylations. It is likely that manipulation of this type of O-Man glycosylation will have wide applications for yeast bioprocessing.
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148
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Yu LM, Xu Y. Epigenetic regulation in cardiac fibrosis. World J Cardiol 2015; 7:784-791. [PMID: 26635926 PMCID: PMC4660473 DOI: 10.4330/wjc.v7.i11.784] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/16/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Cardiac fibrosis represents an adoptive response in the heart exposed to various stress cues. While resolution of the fibrogenic response heralds normalization of heart function, persistent fibrogenesis is usually associated with progressive loss of heart function and eventually heart failure. Cardiac fibrosis is regulated by a myriad of factors that converge on the transcription of genes encoding extracellular matrix proteins, a process the epigenetic machinery plays a pivotal role. In this mini-review, we summarize recent advances regarding the epigenetic regulation of cardiac fibrosis focusing on the role of histone and DNA modifications and non-coding RNAs.
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149
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Protein-Specific Imaging of O-GlcNAcylation in Single Cells. Chembiochem 2015; 16:2571-5. [DOI: 10.1002/cbic.201500544] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 12/15/2022]
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150
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Senescence-Associated Changes in Proteome and O-GlcNAcylation Pattern in Human Peritoneal Mesothelial Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:382652. [PMID: 26640786 PMCID: PMC4657062 DOI: 10.1155/2015/382652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/24/2015] [Accepted: 10/25/2015] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Senescence of peritoneal mesothelial cells represents a biological program defined by arrested cell growth and altered cell secretory phenotype with potential impact in peritoneal dialysis. This study aims to characterize cellular senescence at the level of global protein expression profiles and modification of proteins with O-linked N-acetylglucosamine (O-GlcNAcylation). METHODS A comparative proteomics analysis between young and senescent human peritoneal mesothelial cells (HPMC) was performed using two-dimensional gel electrophoresis. O-GlcNAc status was assessed by Western blot under normal conditions and after modulation with 6-diazo-5-oxo-L-norleucine (DON) to decrease O-GlcNAcylation or O-(2-acetamido-2-deoxy-D-glucopyranosylidene) amino N-phenyl carbamate (PUGNAc) to increase O-GlcNAcylation. RESULTS Comparison of protein pattern of senescent and young HPMC revealed 29 differentially abundant protein spots, 11 of which were identified to be actin (cytoplasmic 1 and 2), cytokeratin-7, cofilin-2, transgelin-2, Hsp60, Hsc70, proteasome β-subunits (type-2 and type-3), nucleoside diphosphate kinase A, and cytosolic 5'(3')-deoxyribonucleotidase. Although the global level of O-GlcNAcylation was comparable, senescent cells were not sensitive to modulation by PUGNAc. DISCUSSION This study identified changes of the proteome and altered dynamics of O-GlcNAc regulation in senescent mesothelial cells. Whereas changes in cytoskeleton-associated proteins likely reflect altered cell morphology, changes in chaperoning and housekeeping proteins may have functional impact on cellular stress response in peritoneal dialysis.
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