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Liu W, Han G, Yin Y, Jiang S, Yu G, Yang Q, Yu W, Ye X, Su Y, Yang Y, Hart GW, Sun H. AANL (Agrocybe aegerita lectin 2) is a new facile tool to probe for O-GlcNAcylation. Glycobiology 2018; 28:363-373. [PMID: 29562282 PMCID: PMC6454498 DOI: 10.1093/glycob/cwy029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 03/10/2018] [Accepted: 03/16/2018] [Indexed: 01/26/2023] Open
Abstract
O-linked N-acetylglucosamine (O-GlcNAcylation) is an important post-translational modification on serine or threonine of proteins, mainly observed in nucleus or cytoplasm. O-GlcNAcylation regulates many cell processes, including transcription, cell cycle, neural development and nascent polypeptide chains stabilization. However, the facile identification of O-GlcNAc is a major bottleneck in O-GlcNAcylation research. Herein, we report that a lectin, Agrocybe aegerita GlcNAc-specific lectin (AANL), also reported as AAL2, can be used as a powerful probe for O-GlcNAc identification. Glycan array analyses and surface plasmon resonance (SPR) assays show that AANL binds to GlcNAc with a dissociation constant (KD) of 94.6 μM, which is consistent with the result tested through isothiocyanate (ITC) assay reported before (Jiang S, Chen Y, Wang M, Yin Y, Pan Y, Gu B, Yu G, Li Y, Wong BH, Liang Y, et al. 2012. A novel lectin from Agrocybe aegerita shows high binding selectivity for terminal N-acetylglucosamine. Biochem J. 443:369-378.). Confocal imaging shows that AANL co-localizes extensively with NUP62, a heavily O-GlcNAcylated and abundant nuclear pore glycoprotein. Furthermore, O-GlcNAc-modified peptides could be effectively enriched in the late flow-through peak from simple samples by using affinity columns Sepharose 4B-AANL or POROS-AANL. Therefore, using AANL affinity column, we identified 28 high-confidence O-linked HexNAc-modified peptides mapped on 17 proteins involving diverse cellular progresses, including transcription, hydrolysis progress, urea cycle, alcohol metabolism and cell cycle. And most importantly, major proteins and sites were not annotated in the dbOGAP database. These results suggest that the AANL lectin is a new useful tool for enrichment and identification of O-GlcNAcylated proteins and peptides.
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Affiliation(s)
- Wei Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Guanghui Han
- Department of Biological Chemistry, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yalin Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Shuai Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Guojun Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Qing Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Wenhui Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Xiangdong Ye
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Yanting Su
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Yajun Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
| | - Gerald W Hart
- Department of Biological Chemistry, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hui Sun
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University
- Hubei Province key Laboratory of Allergy and Immunology
- Key laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan 430071, Hubei Province, P. R. China
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Smet-Nocca C, Page A, Cantrelle FX, Nikolakaki E, Landrieu I, Giannakouros T. The O-β-linked N-acetylglucosaminylation of the Lamin B receptor and its impact on DNA binding and phosphorylation. Biochim Biophys Acta Gen Subj 2018; 1862:825-835. [PMID: 29337275 DOI: 10.1016/j.bbagen.2018.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/24/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
Lamin B Receptor (LBR) is an integral protein of the interphase inner nuclear membrane that is implicated in chromatin anchorage to the nuclear envelope. Phosphorylation of a stretch of arginine-serine (RS) dipeptides in the amino-terminal nucleoplasmic domain of LBR regulates the interactions of the receptor with other nuclear proteins, DNA and RNA and thus modulates tethering of heterochromatin to the nuclear envelope. While phosphorylation has been extensively studied, very little is known about other post-translational modifications of the protein. There is only one report on the O-β-linked N-acetyl-glucosaminylation (O-GlcNAcylation) of a serine residue downstream of the RS domain of rat LBR. In the present study we identify additional O-GlcNAcylation sites by using as substrates of O-β-N-acetylglucosaminyltransferase (OGT) a set of peptides containing the entire LBR RS domain or parts of it as well as flanking sequences. The in vitro activity of OGT was assessed by tandem mass spectrometry and NMR spectroscopy. Furthermore, we provide evidence that O-GlcNAcylation hampers DNA binding while it marginally affects RS domain phosphorylation mediated by SRPK1, Akt2 and cdk1 kinases. GENERAL SIGNIFICANCE Our methodology providing a quantitative description of O-GlcNAc patterns based on a combination of mass spectrometry and high resolution NMR spectroscopy on short peptide substrates allows subsequent functional analyses. Hence, our approach is of general interest to a wide audience of biologists aiming at deciphering the functional role of O-GlcNAc glycosylation and its crosstalk with phosphorylation.
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Affiliation(s)
- Caroline Smet-Nocca
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France.
| | - Adeline Page
- Proteomics Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Strasbourg University, Illkirch, France
| | - François-Xavier Cantrelle
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Eleni Nikolakaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Isabelle Landrieu
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Thomas Giannakouros
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University of Thessaloniki, 54124 Thessaloniki, Greece
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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Hoter A, Amiri M, Prince A, Amer H, Warda M, Naim HY. Differential Glycosylation and Modulation of Camel and Human HSP Isoforms in Response to Thermal and Hypoxic Stresses. Int J Mol Sci 2018; 19:ijms19020402. [PMID: 29385708 PMCID: PMC5855624 DOI: 10.3390/ijms19020402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 01/11/2023] Open
Abstract
Increased expression of heat shock proteins (HSPs) following heat stress or other stress conditions is a common physiological response in almost all living organisms. Modification of cytosolic proteins including HSPs by O-GlcNAc has been shown to enhance their capabilities for counteracting lethal levels of cellular stress. Since HSPs are key players in stress resistance and protein homeostasis, we aimed to analyze their forms at the cellular and molecular level using camel and human HSPs as models for efficient and moderate thermotolerant mammals, respectively. In this study, we cloned the cDNA encoding two inducible HSP members, HSPA6 and CRYAB from both camel (Camelus dromedarius) and human in a Myc-tagged mammalian expression vector. Expression of these chaperones in COS-1 cells revealed protein bands of approximately 25-kDa for both camel and human CRYAB and 70-kDa for camel HSPA6 and its human homologue. While localization and trafficking of the camel and human HSPs revealed similar cytosolic localization, we could demonstrate altered glycan structure between camel and human HSPA6. Interestingly, the glycoform of camel HSPA6 was rapidly formed and stabilized under normal and stress culture conditions whereas human HSPA6 reacted differently under similar thermal and hypoxic stress conditions. Our data suggest that efficient glycosylation of camel HSPA6 is among the mechanisms that provide camelids with a superior capability for alleviating stressful environmental circumstances.
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Affiliation(s)
- Abdullah Hoter
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
| | - Mahdi Amiri
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
| | - Abdelbary Prince
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
| | - Hassan Amer
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
| | - Mohamad Warda
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
| | - Hassan Y Naim
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
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Nagnan-Le Meillour P, Joly A, Le Danvic C, Marie A, Zirah S, Cornard JP. Binding Specificity of Native Odorant-Binding Protein Isoforms Is Driven by Phosphorylation and O-N-Acetylglucosaminylation in the Pig Sus scrofa. Front Endocrinol (Lausanne) 2018; 9:816. [PMID: 30740091 PMCID: PMC6355697 DOI: 10.3389/fendo.2018.00816] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/27/2018] [Indexed: 11/16/2022] Open
Abstract
Odorant-binding proteins (OBP) are secreted in the nasal mucus at the vicinity of olfactory receptors (ORs). They act, at least, as an interface between hydrophobic and volatile odorant molecules and the hydrophilic medium bathing the ORs. They have also been hypothesized to be part of the molecular coding of odors and pheromones, by forming specific complexes with odorant molecules that could ultimately stimulate ORs to trigger the olfactory transduction cascade. In a previous study, we have evidenced that pig olfactory secretome was composed of numerous olfactory binding protein isoforms, generated by O-GlcNAcylation and phosphorylation. In addition, we have shown that recombinant OBP (stricto sensu) produced in yeast is made up of a mixture of isoforms that differ in their phosphorylation pattern, which in turn determines binding specificity. Taking advantage of the high amount of OBP secreted by a single animal, we performed a similar study, under exactly the same experimental conditions, on native isoforms isolated from pig, Sus scrofa, nasal tissue. Four fractions were obtained by using strong anion exchange HPLC. Mapping of phosphorylation and O-GlcNAcylation sites by CID-nanoLC-MS/MS allowed unambiguous localization of phosphosites at S13 and T122 and HexNAc sites at S13 and S19. T112 or T115 could also be phosphorylated. BEMAD analysis suggested extra phosphosites located at S23, S24, S41, S49, S57, S67, and T71. Due to the very low stoichiometry of GlcNAc-peptides and phosphopeptides, these sites were identified on total mixture of OBP isoforms instead of HPLC-purified OBP isoforms. Nevertheless, binding properties of native OBP isoforms to specific ligands in S. scrofa were monitored by fluorescence spectroscopy. Recombinant phosphorylated OBP-Pichia isoforms bind steroids and fatty acids with slight differences. Native isoforms, that are phosphorylated but also O-GlcNAcylated show radically different binding affinities for the same compounds, which strongly suggests that O-GlcNAcylation increases the binding specificity of OBP isoforms. These findings extend the role of O-GlcNAc in regulating the function of proteins involved in many mechanisms of metabolic homeostasis, including extracellular signaling in olfaction. Data is available via ProteomeXChange with identifier PXD011371.
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Affiliation(s)
- Patricia Nagnan-Le Meillour
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576, USC-UGSF INRA 1409, CNRS-Université de Lille, Lille, France
- *Correspondence: Patricia Nagnan-Le Meillour
| | - Alexandre Joly
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576, USC-UGSF INRA 1409, CNRS-Université de Lille, Lille, France
| | - Chrystelle Le Danvic
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576, USC-UGSF INRA 1409, CNRS-Université de Lille, Lille, France
- ALLICE R&D, Paris, France
| | - Arul Marie
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, UMR 7245 CNRS/MNHN, Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, UMR 7245 CNRS/MNHN, Paris, France
| | - Jean-Paul Cornard
- Laboratoire de Spectroscopie Infrarouge et Raman, UMR8516 CNRS-Université de Lille, Lille, France
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Lambert M, Bastide B, Cieniewski-Bernard C. Involvement of O-GlcNAcylation in the Skeletal Muscle Physiology and Physiopathology: Focus on Muscle Metabolism. Front Endocrinol (Lausanne) 2018; 9:578. [PMID: 30459708 PMCID: PMC6232757 DOI: 10.3389/fendo.2018.00578] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle represents around 40% of whole body mass. The principal function of skeletal muscle is the conversion of chemical energy toward mechanic energy to ensure the development of force, provide movement and locomotion, and maintain posture. This crucial energy dependence is maintained by the faculty of the skeletal muscle for being a central place as a "reservoir" of amino acids and carbohydrates in the whole body. A fundamental post-translational modification, named O-GlcNAcylation, depends, inter alia, on these nutrients; it consists to the transfer or the removal of a unique monosaccharide (N-acetyl-D-glucosamine) to a serine or threonine hydroxyl group of nucleocytoplasmic and mitochondrial proteins in a dynamic process by the O-GlcNAc Transferase (OGT) and the O-GlcNAcase (OGA), respectively. O-GlcNAcylation has been shown to be strongly involved in crucial intracellular mechanisms through the modulation of signaling pathways, gene expression, or cytoskeletal functions in various organs and tissues, such as the brain, liver, kidney or pancreas, and linked to the etiology of associated diseases. In recent years, several studies were also focused on the role of O-GlcNAcylation in the physiology and the physiopathology of skeletal muscle. These studies were mostly interested in O-GlcNAcylation during muscle exercise or muscle-wasting conditions. Major findings pointed out a different "O-GlcNAc signature" depending on muscle type metabolism at resting, wasting and exercise conditions, as well as depending on acute or long-term exhausting exercise protocol. First insights showed some differential OGT/OGA expression and/or activity associated with some differential stress cellular responses through Reactive Oxygen Species and/or Heat-Shock Proteins. Robust data displayed that these O-GlcNAc changes could lead to (i) a differential modulation of the carbohydrates metabolism, since the majority of enzymes are known to be O-GlcNAcylated, and to (ii) a differential modulation of the protein synthesis/degradation balance since O-GlcNAcylation regulates some key signaling pathways such as Akt/GSK3β, Akt/mTOR, Myogenin/Atrogin-1, Myogenin/Mef2D, Mrf4 and PGC-1α in the skeletal muscle. Finally, such involvement of O-GlcNAcylation in some metabolic processes of the skeletal muscle might be linked to some associated diseases such as type 2 diabetes or neuromuscular diseases showing a critical increase of the global O-GlcNAcylation level.
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Cox NJ, Luo PM, Smith TJ, Bisnett BJ, Soderblom EJ, Boyce M. A Novel Glycoproteomics Workflow Reveals Dynamic O-GlcNAcylation of COPγ1 as a Candidate Regulator of Protein Trafficking. Front Endocrinol (Lausanne) 2018; 9:606. [PMID: 30459710 PMCID: PMC6232944 DOI: 10.3389/fendo.2018.00606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/24/2018] [Indexed: 02/04/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) is an abundant and essential intracellular form of protein glycosylation in animals and plants. In humans, dysregulation of O-GlcNAcylation occurs in a wide range of diseases, including cancer, diabetes, and neurodegeneration. Since its discovery more than 30 years ago, great strides have been made in understanding central aspects of O-GlcNAc signaling, including identifying thousands of its substrates and characterizing the enzymes that govern it. However, while many O-GlcNAcylated proteins have been reported, only a small subset of these change their glycosylation status in response to a typical stimulus or stress. Identifying the functionally important O-GlcNAcylation changes in any given signaling context remains a significant challenge in the field. To address this need, we leveraged chemical biology and quantitative mass spectrometry methods to create a new glycoproteomics workflow for profiling stimulus-dependent changes in O-GlcNAcylated proteins. In proof-of-principle experiments, we used this new workflow to interrogate changes in O-GlcNAc substrates in mammalian protein trafficking pathways. Interestingly, our results revealed dynamic O-GlcNAcylation of COPγ1, an essential component of the coat protein I (COPI) complex that mediates Golgi protein trafficking. Moreover, we detected 11 O-GlcNAc moieties on COPγ1 and found that this modification is reduced by a model secretory stress that halts COPI trafficking. Our results suggest that O-GlcNAcylation may regulate the mammalian COPI system, analogous to its previously reported roles in other protein trafficking pathways. More broadly, our glycoproteomics workflow is applicable to myriad systems and stimuli, empowering future studies of O-GlcNAc in a host of biological contexts.
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Affiliation(s)
- Nathan J. Cox
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Peter M. Luo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Timothy J. Smith
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Brittany J. Bisnett
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Erik J. Soderblom
- Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: Michael Boyce
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Lopez Aguilar A, Gao Y, Hou X, Lauvau G, Yates JR, Wu P. Profiling of Protein O-GlcNAcylation in Murine CD8 + Effector- and Memory-like T Cells. ACS Chem Biol 2017; 12:3031-3038. [PMID: 29125738 DOI: 10.1021/acschembio.7b00869] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During an acute infection, antigenic stimulation leads to activation, expansion, and differentiation of naïve CD8+ T cells, first into cytotoxic effector cells and eventually into long-lived memory cells. T cell antigen receptors (TCRs) detect antigens on antigen-presenting cells (APCs) in the form of antigenic peptides bound to major histocompatibility complex I (MHC-I)-encoded molecules and initiate TCR signal transduction network. This process is mediated by phosphorylation of many intracellular signaling proteins. Protein O-GlcNAc modification is another post-translational modification involved in this process, which often has either reciprocal or synergistic roles with phosphorylation. In this study, using a chemoenzymatic glycan labeling technique and proteomics analysis, we compared protein O-GlcNAcylation of murine effector and memory-like CD8+ T cells differentiated in vitro. By quantitative proteomics analysis, we identified 445 proteins that are significantly regulated in either effector- or memory-like T cell subsets. Furthermore, qualitative and quantitative analysis identified highly regulated protein clusters that suggest involvement of this post-translational modification in specific cellular processes. In effector-like T cells, protein O-GlcNAcylation is heavily involved in transcriptional and translational processes that drive fast effector T cells proliferation. During the formation of memory-like T cells, protein O-GlcNAcylation is involved in a more specific, perhaps more targeted regulation of transcription, mRNA processing, and translation. Significantly, O-GlcNAc plays a critical role as part of the "histone code" in both CD8+ T cells subgroups.
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Affiliation(s)
- Aime Lopez Aguilar
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yu Gao
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xiaomeng Hou
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gregoire Lauvau
- Department
of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - John R. Yates
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peng Wu
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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Kupferschmid M, Aquino-Gil MO, Shams-Eldin H, Schmidt J, Yamakawa N, Krzewinski F, Schwarz RT, Lefebvre T. Identification of O-GlcNAcylated proteins in Plasmodium falciparum. Malar J 2017; 16:485. [PMID: 29187233 PMCID: PMC5707832 DOI: 10.1186/s12936-017-2131-2] [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: 07/17/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Post-translational modifications (PTMs) constitute a huge group of chemical modifications increasing the complexity of the proteomes of living beings. PTMs have been discussed as potential anti-malarial drug targets due to their involvement in many cell processes. O-GlcNAcylation is a widespread PTM found in different organisms including Plasmodium falciparum. The aim of this study was to identify O-GlcNAcylated proteins of P. falciparum, to learn more about the modification process and to understand its eventual functions in the Apicomplexans. METHODS The P. falciparum strain 3D7 was amplified in erythrocytes and purified. The proteome was checked for O-GlcNAcylation using different methods. The level of UDP-GlcNAc, the donor of the sugar moiety for O-GlcNAcylation processes, was measured using high-pH anion exchange chromatography. O-GlcNAcylated proteins were enriched and purified utilizing either click chemistry labelling or adsorption on succinyl-wheat germ agglutinin beads. Proteins were then identified by mass-spectrometry (nano-LC MS/MS). RESULTS While low when compared to MRC5 control cells, P. falciparum disposes of its own pool of UDP-GlcNAc. By using proteomics methods, 13 O-GlcNAcylated proteins were unambiguously identified (11 by click-chemistry and 6 by sWGA-beads enrichment; 4 being identified by the 2 approaches) in late trophozoites. These proteins are all part of pathways, functions and structures important for the parasite survival. By probing clicked-proteins with specific antibodies, Hsp70 and α-tubulin were identified as P. falciparum O-GlcNAc-bearing proteins. CONCLUSIONS This study is the first report on the identity of P. falciparum O-GlcNAcylated proteins. While the parasite O-GlcNAcome seems close to those of other species, the structural differences exhibited by the proteomes provides a glimpse of innovative therapeutic paths to fight malaria. Blocking biosynthesis of UDP-GlcNAc in the parasites is another promising option to reduce Plasmodium life cycle.
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Affiliation(s)
- Mattis Kupferschmid
- Institute for Virology, Laboratory of Parasitology, Philipps-University, Marburg, Germany
| | - Moyira Osny Aquino-Gil
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.,Instituto Tecnológico de Oaxaca, Tecnológico Nacional de México, Oaxaca, Mexico.,Centro de Investigación UNAM-UABJO, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, Mexico
| | - Hosam Shams-Eldin
- Institute for Virology, Laboratory of Parasitology, Philipps-University, Marburg, Germany
| | - Jörg Schmidt
- Institute for Virology, Laboratory of Parasitology, Philipps-University, Marburg, Germany
| | - Nao Yamakawa
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Frédéric Krzewinski
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Ralph T Schwarz
- Institute for Virology, Laboratory of Parasitology, Philipps-University, Marburg, Germany.,Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Tony Lefebvre
- Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.
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Bao W, You ZH, Huang DS. CIPPN: computational identification of protein pupylation sites by using neural network. Oncotarget 2017; 8:108867-108879. [PMID: 29312575 PMCID: PMC5752488 DOI: 10.18632/oncotarget.22335] [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: 07/14/2017] [Accepted: 09/03/2017] [Indexed: 11/25/2022] Open
Abstract
Recently, experiments revealed the pupylation to be a signal for the selective regulation of proteins in several serious human diseases. As one of the most significant post translational modification in the field of biology and disease, pupylation has the ability to playing the key role in the regulation various diseases’ biological processes. Meanwhile, effectively identification such type modification will be helpful for proteins to perform their biological functions and contribute to understanding the molecular mechanism, which is the foundation of drug design. The existing algorithms of identification such types of modified sites often have some defects, such as low accuracy and time-consuming. In this research, the pupylation sites’ identification model, CIPPN, demonstrates better performance than other existing approaches in this field. The proposed predictor achieves Acc value of 89.12 and Mcc value of 0.7949 in 10-fold cross-validation tests in the Pupdb Database (http://cwtung.kmu.edu.tw/pupdb). Significantly, such algorithm not only investigates the sequential, structural and evolutionary hallmarks around pupylation sites but also compares the differences of pupylation from the environmental, conservative and functional characterization of substrates. Therefore, the proposed feature description approach and algorithm results prove to be useful for further experimental investigation of such modification’s identification.
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Affiliation(s)
- Wenzheng Bao
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Zhu-Hong You
- Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
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61
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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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62
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Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase. Nat Chem Biol 2017; 13:1267-1273. [PMID: 29058723 PMCID: PMC5698155 DOI: 10.1038/nchembio.2494] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 09/07/2017] [Indexed: 12/17/2022]
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is an essential human glycosyltransferase that adds O-GlcNAc modifications to numerous proteins. However, little is known about the mechanism with which OGT recognizes various protein substrates. Here we report on GlcNAc electrophilic probes (GEPs) to expedite the characterization of OGT-substrate recognition. Data from mass spectrometry, X-ray crystallization, and biochemical and radiolabeled kinetic assays support the application of GEPs to rapidly report the impacts of OGT mutations on protein substrate or sugar binding and to discover OGT residues crucial for protein recognition. Interestingly, we found that the same residues on the inner surface of the N-terminal domain contribute to OGT interactions with different protein substrates. By tuning reaction conditions, a GEP enables crosslinking of OGT with acceptor substrates in situ, affording a unique method to discover genuine substrates that weakly or transiently interact with OGT. Hence, GEPs provide new strategies to dissect OGT-substrate binding and recognition.
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63
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Quantitative analysis of O-GlcNAcylation in combination with isobaric tag labeling and chemoenzymatic enrichment. Bioorg Med Chem Lett 2017; 27:5022-5026. [PMID: 29029932 DOI: 10.1016/j.bmcl.2017.10.005] [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: 07/13/2017] [Revised: 09/30/2017] [Accepted: 10/03/2017] [Indexed: 11/21/2022]
Abstract
Protein O-GlcNAcylation regulates various biological processes, and is associated with several diseases. Therefore, the development of quantitative proteomics is important for understanding the mechanisms of O-GlcNAc-related diseases. We previously reported selective enrichment of O-GlcNAcylated peptides, which provided high-selectivity and effective release by a novel thiol-alkyne and thiol-disulfide exchange. Here, we describe a new approach using initial isobaric tag labeling for relative quantification followed by enrichment and β-elimination/Michael addition with dithiothreitol for identification of both proteins and modification sites. The approach was validated using model proteins and peptides. This novel strategy could be used for quantitative O-GlcNAcome of biological samples.
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64
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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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65
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Britto-Borges T, Barton GJ. A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase. PLoS One 2017; 12:e0184405. [PMID: 28886091 PMCID: PMC5590929 DOI: 10.1371/journal.pone.0184405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/23/2017] [Indexed: 01/17/2023] Open
Abstract
Protein O-GlcNAcylation (O-GlcNAc) is an essential post-translational modification (PTM) in higher eukaryotes. The O-linked β-N-acetylglucosamine transferase (OGT), targets specific Serines and Threonines (S/T) in intracellular proteins. However, unlike phosphorylation, fewer than 25% of known O-GlcNAc sites match a clear sequence pattern. Accordingly, the three-dimensional structures of O-GlcNAc sites were characterised to investigate the role of structure in molecular recognition. From 1,584 O-GlcNAc sites in 620 proteins, 143 were mapped to protein structures determined by X-ray crystallography. The modified S/T were 1.7 times more likely to be annotated in the REM465 field which defines missing residues in a protein structure, while 7 O-GlcNAc sites were solvent inaccessible and unlikely to be targeted by OGT. 132 sites with complete backbone atoms clustered into 10 groups, but these were indistinguishable from clusters from unmodified S/T. This suggests there is no prevalent three-dimensional motif for OGT recognition. Predicted features from the 620 proteins were compared to unmodified S/T in O-GlcNAcylated proteins and globular proteins. The Jpred4 predicted secondary structure shows that modified S/T were more likely to be coils. 5/6 methods to predict intrinsic disorder indicated O-GlcNAcylated S/T to be significantly more disordered than unmodified S/T. Although the analysis did not find a pattern in the site three-dimensional structure, it revealed the residues around the modification site are likely to be disordered and suggests a potential role of secondary structure elements in OGT site recognition.
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Affiliation(s)
- Thiago Britto-Borges
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Geoffrey J. Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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66
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Nikolakaki E, Mylonis I, Giannakouros T. Lamin B Receptor: Interplay between Structure, Function and Localization. Cells 2017; 6:cells6030028. [PMID: 28858257 PMCID: PMC5617974 DOI: 10.3390/cells6030028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/15/2022] Open
Abstract
Lamin B receptor (LBR) is an integral protein of the inner nuclear membrane, containing a hydrophilic N-terminal end protruding into the nucleoplasm, eight hydrophobic segments that span the membrane and a short, nucleoplasmic C-terminal tail. Two seemingly unrelated functions have been attributed to LBR. Its N-terminal domain tethers heterochromatin to the nuclear periphery, thus contributing to the shape of interphase nuclear architecture, while its transmembrane domains exhibit sterol reductase activity. Mutations within the transmembrane segments result in defects in cholesterol synthesis and are associated with diseases such as the Pelger–Huët anomaly and Greenberg skeletal dysplasia, whereas no such harmful mutations related to the anchoring properties of LBR have been reported so far. Recent evidence suggests a dynamic regulation of LBR expression levels, structural organization, localization and function, in response to various signals. The molecular mechanisms underlying this dynamic behavior have not yet been fully unraveled. Here, we provide an overview of the current knowledge of the interplay between the structure, function and localization of LBR, and hint at the interconnection of the two distinct functions of LBR.
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Affiliation(s)
- Eleni Nikolakaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University, Thessaloniki 54124, Greece.
| | - Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Panepistimiou 3 BIOPOLIS, Larissa 41500, Greece.
| | - Thomas Giannakouros
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University, Thessaloniki 54124, Greece.
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67
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Leney AC, Rafie K, van Aalten DMF, Heck AJR. Direct Monitoring of Protein O-GlcNAcylation by High-Resolution Native Mass Spectrometry. ACS Chem Biol 2017; 12:2078-2084. [PMID: 28609614 PMCID: PMC5565903 DOI: 10.1021/acschembio.7b00371] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
O-GlcNAcylation is one of the most
abundant metazoan nuclear-cytoplasmic post-translational modifications.
Proteins modified by O-GlcNAc play key cellular roles in signaling,
transcription, metabolism, and cell division. Mechanistic studies
on protein O-GlcNAcylation are hampered by the lack of methods that
can simultaneously quantify O-GlcNAcylation, determine its stoichiometry,
and monitor O-GlcNAcylation kinetics. Here, we demonstrate that high-resolution
native mass spectrometry can be employed to monitor the small mass
shifts induced by modification by O-GlcNAc on two known protein substrates,
CK2α and TAB1, without the need for radioactive labeling or
chemoenzymatic tagging using large mass tags. Limited proteolysis
enabled further localization of the O-GlcNAc sites. In peptide-centric
MS analysis, the O-GlcNAc moiety is known to be easily lost. In contrast,
we demonstrate that the O-GlcNAc is retained under native MS conditions,
enabling precise quantitative analysis of stoichiometry and O-GlcNAcylation
kinetics. Together, the data highlight that high resolution native
MS may provide an alternative tool to monitor kinetics on one of the
most labile of protein post-translational modifications, in an efficient,
reliable, and quantitative manner.
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Affiliation(s)
- Aneika C. Leney
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences and Netherlands
Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Karim Rafie
- School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, United Kingdom
| | - Daan M. F. van Aalten
- School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, United Kingdom
| | - Albert J. R. Heck
- Biomolecular Mass
Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences and Netherlands
Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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68
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017. [PMID: 28585084 DOI: 10.1007/s00216-017-04067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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69
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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70
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Selvan N, Williamson R, Mariappa D, Campbell DG, Gourlay R, Ferenbach AT, Aristotelous T, Hopkins-Navratilova I, Trost M, van Aalten DMF. A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nat Chem Biol 2017; 13:882-887. [PMID: 28604694 DOI: 10.1038/nchembio.2404] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 03/14/2017] [Indexed: 01/09/2023]
Abstract
Protein O-GlcNAcylation is a reversible post-translational modification of serines and threonines on nucleocytoplasmic proteins. It is cycled by the enzymes O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (O-GlcNAcase or OGA). Genetic approaches in model organisms have revealed that protein O-GlcNAcylation is essential for early embryogenesis. The Drosophila melanogaster gene supersex combs (sxc), which encodes OGT, is a polycomb gene, whose null mutants display homeotic transformations and die at the pharate adult stage. However, the identities of the O-GlcNAcylated proteins involved and the underlying mechanisms linking these phenotypes to embryonic development are poorly understood. Identification of O-GlcNAcylated proteins from biological samples is hampered by the low stoichiometry of this modification and by limited enrichment tools. Using a catalytically inactive bacterial O-GlcNAcase mutant as a substrate trap, we have enriched the O-GlcNAc proteome of the developing Drosophila embryo, identifying, among others, known regulators of Hox genes as candidate conveyors of OGT function during embryonic development.
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Affiliation(s)
- Nithya Selvan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Ritchie Williamson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Tonia Aristotelous
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Iva Hopkins-Navratilova
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
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71
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Xiao H, Wu R. Global and Site-Specific Analysis Revealing Unexpected and Extensive Protein S-GlcNAcylation in Human Cells. Anal Chem 2017; 89:3656-3663. [PMID: 28234450 DOI: 10.1021/acs.analchem.6b05064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein glycosylation is highly diverse and essential for mammalian cell survival. Heterogeneous glycans may be bound to different amino acid residues, forming multiple types of protein glycosylation. In this work, unexpected protein S-GlcNAcylation on cysteine residues was observed to extensively exist in human cells through global and site-specific analysis of protein GlcNAcylation by mass spectrometry. Three independent experiments produced similar results of many cysteine residues bound to N-acetylglucosamine (GlcNAc). Among well-localized S-GlcNAcylation sites, several motifs with an acidic amino acid around the sites were identified, which strongly suggests that a particular type of enzyme is responsible for this modification. Clustering results show that glycoproteins modified with S-GlcNAc are mainly involved in cell-cell adhesion and gene expression. For the first time, we found that proteins were extensively bound to GlcNAc through the side chains of cysteine residues in human cells, and the current discovery further advances our understanding of protein glycosylation.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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72
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Kamemura K. O-GlcNAc glycosylation stoichiometry of the FET protein family: only EWS is glycosylated with a high stoichiometry. Biosci Biotechnol Biochem 2017; 81:541-546. [DOI: 10.1080/09168451.2016.1263148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
Of the FET (fused in sarcoma [FUS]/Ewing sarcoma protein [EWS]/TATA binding protein-associated factor 15 [TAF15]) family of heterogeneous nuclear ribonucleoprotein particle proteins, FUS and TAF15 are consistently and EWS variably found in inclusion bodies in neurodegenerative diseases such as frontotemporal lobar degeneration associated with FUS. It is speculated that dysregulation of FET proteins at the post-translational level is involved in their cytoplasmic deposition. Here, the O-linked β-N-acetylglucosamine (O-GlcNAc) glycosylation stoichiometry of the FET proteins was chemoenzymatically analyzed, and it was found that only EWS is dynamically glycosylated with a high stoichiometry in the neural cell lines tested and in mouse brain. It was also confirmed that EWS, but not FUS and TAF15, is glycosylated with a high stoichiometry not only in the neural cells but also in the non-neural cell lines tested. These results indicate that O-GlcNAc glycosylation imparts a physicochemical property on EWS that is distinct from that of the other FET proteins in most of cell lineages or tissues.
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Affiliation(s)
- Kazuo Kamemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
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73
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Ma J, Hart GW. Analysis of Protein O-GlcNAcylation by Mass Spectrometry. ACTA ACUST UNITED AC 2017; 87:24.10.1-24.10.16. [PMID: 28150883 DOI: 10.1002/cpps.24] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
O-linked β-D-N-acetyl glucosamine (O-GlcNAc) addition (O-GlcNAcylation), a post-translational modification of serine/threonine residues of proteins, is involved in diverse cellular metabolic and signaling pathways. Aberrant O-GlcNAcylation underlies the initiation and progression of multiple chronic diseases including diabetes, cancer, and neurodegenerative diseases. Numerous methods have been developed for the analysis of protein O-GlcNAcylation, but instead of discussing the classical biochemical techniques, this unit covers O-GlcNAc characterization by combining several enrichment methods and mass spectrometry detection techniques [including collision-induced dissociation (CID), higher energy collision dissociation (HCD), and electron transfer dissociation (ETD) mass spectrometry]. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Junfeng Ma
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Gerald W Hart
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
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74
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Shen DL, Liu TW, Zandberg W, Clark T, Eskandari R, Alteen MG, Tan HY, Zhu Y, Cecioni S, Vocadlo D. Catalytic Promiscuity of O-GlcNAc Transferase Enables Unexpected Metabolic Engineering of Cytoplasmic Proteins with 2-Azido-2-deoxy-glucose. ACS Chem Biol 2017; 12:206-213. [PMID: 27935279 DOI: 10.1021/acschembio.6b00876] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
O-GlcNAc transferase (OGT) catalyzes the installation of N-acetylglucosamine (GlcNAc) O-linked to nucleocytoplasmic proteins (O-GlcNAc) within multicellular eukaryotes. OGT shows surprising tolerance for structural changes in the sugar component of its nucleotide sugar donor substrate, uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). Here, we find that OGT uses UDP-glucose to install O-linked glucose (O-Glc) onto proteins only 25-fold less efficiently than O-GlcNAc. Spurred by this observation, we show that OGT transfers 2-azido-2-deoxy-d-glucose (GlcAz) in vitro from UDP-GlcAz to proteins. Further, feeding cells with per-O-acetyl GlcAz (AcGlcAz), in combination with inhibition or inducible knockout of OGT, shows OGT-dependent modification of nuclear and cytoplasmic proteins with O-GlcAz as detected using microscopy, immunoblot, and proteomics. We find that O-GlcAz is reversible within cells, and an unidentified cellular enzyme exists to cleave O-Glc that can also process O-GlcAz. We anticipate that AcGlcAz will prove to be a useful tool to study the O-GlcNAc modification. We also speculate that, given the high concentration of UDP-Glc within certain mammalian tissues, O-Glc may exist within mammals and serve as a physiologically relevant modification.
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Affiliation(s)
- David L. Shen
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ta-Wei Liu
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Wesley Zandberg
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Tom Clark
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Razieh Eskandari
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew G. Alteen
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Hong Yee Tan
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yanping Zhu
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Samy Cecioni
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David Vocadlo
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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75
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Kamemura K, Abe H. The glycosylation stoichiometry of EWS species in neuronal cells. Biosci Biotechnol Biochem 2017; 81:165-167. [DOI: 10.1080/09168451.2016.1230004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Although Ewing sarcoma protein (EWS) is known to be glycosylated by O-linked β-N-acetylglucosamine (O-GlcNAc), the dynamics and stoichiometry of its glycosylation remain obscure. Here, we report a dynamic change in the glycosylation stoichiometry of EWS species during neuronal differentiation of embryonic carcinoma P19 cells. Our findings suggest that O-GlcNAc glycosylation participates in the regulation of EWS functions in neuronal cells.
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Affiliation(s)
- Kazuo Kamemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Hiromi Abe
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
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76
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Qin CX, Sleaby R, Davidoff AJ, Bell JR, De Blasio MJ, Delbridge LM, Chatham JC, Ritchie RH. Insights into the role of maladaptive hexosamine biosynthesis and O-GlcNAcylation in development of diabetic cardiac complications. Pharmacol Res 2016; 116:45-56. [PMID: 27988387 DOI: 10.1016/j.phrs.2016.12.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/28/2016] [Accepted: 12/13/2016] [Indexed: 12/21/2022]
Abstract
Diabetes mellitus significantly increases the risk of heart failure, independent of coronary artery disease. The mechanisms implicated in the development of diabetic heart disease, commonly termed diabetic cardiomyopathy, are complex, but much of the impact of diabetes on the heart can be attributed to impaired glucose handling. It has been shown that the maladaptive nutrient-sensing hexosamine biosynthesis pathway (HBP) contributes to diabetic complications in many non-cardiac tissues. Glucose metabolism by the HBP leads to enzymatically-regulated, O-linked attachment of a sugar moiety molecule, β-N-acetylglucosamine (O-GlcNAc), to proteins, affecting their biological activity (similar to phosphorylation). In normal physiology, transient activation of HBP/O-GlcNAc mechanisms is an adaptive, protective means to enhance cell survival; interventions that acutely suppress this pathway decrease tolerance to stress. Conversely, chronic dysregulation of HBP/O-GlcNAc mechanisms has been shown to be detrimental in certain pathological settings, including diabetes and cancer. Most of our understanding of the impact of sustained maladaptive HBP and O-GlcNAc protein modifications has been derived from adipose tissue, skeletal muscle and other non-cardiac tissues, as a contributing mechanism to insulin resistance and progression of diabetic complications. However, the long-term consequences of persistent activation of cardiac HBP and O-GlcNAc are not well-understood; therefore, the goal of this timely review is to highlight current understanding of the role of the HBP pathway in development of diabetic cardiomyopathy.
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Affiliation(s)
- Cheng Xue Qin
- Heart Failure Pharmacology, Baker IDI Heart & Diabetes Institute, Melbourne VIC 3004, Australia; Department of Pharmacology, University of Melbourne, VIC 3010, Australia
| | - Rochelle Sleaby
- Heart Failure Pharmacology, Baker IDI Heart & Diabetes Institute, Melbourne VIC 3004, Australia; Department of Physiology, University of Melbourne, VIC 3010, Australia
| | - Amy J Davidoff
- University of New England, Biddeford, ME, 04072, United States
| | - James R Bell
- Department of Physiology, University of Melbourne, VIC 3010, Australia
| | - Miles J De Blasio
- Heart Failure Pharmacology, Baker IDI Heart & Diabetes Institute, Melbourne VIC 3004, Australia; School of BioSciences, University of Melbourne, VIC 3010, Australia
| | | | - John C Chatham
- University of Alabama at Birmingham, Birmingham, AL, 35233, United States
| | - Rebecca H Ritchie
- Heart Failure Pharmacology, Baker IDI Heart & Diabetes Institute, Melbourne VIC 3004, Australia; Department of Pharmacology, University of Melbourne, VIC 3010, Australia; Department of Medicine, Monash University, Clayton 3800, VIC, Australia.
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77
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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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78
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Lund PJ, Elias JE, Davis MM. Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:3086-3098. [PMID: 27655845 DOI: 10.4049/jimmunol.1502031] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
Abstract
T cell activation in response to Ag is largely regulated by protein posttranslational modifications. Although phosphorylation has been extensively characterized in T cells, much less is known about the glycosylation of serine/threonine residues by O-linked N-acetylglucosamine (O-GlcNAc). Given that O-GlcNAc appears to regulate cell signaling pathways and protein activity similarly to phosphorylation, we performed a comprehensive analysis of O-GlcNAc during T cell activation to address the functional importance of this modification and to identify the modified proteins. Activation of T cells through the TCR resulted in a global elevation of O-GlcNAc levels and in the absence of O-GlcNAc, IL-2 production and proliferation were compromised. T cell activation also led to changes in the relative expression of O-GlcNAc transferase (OGT) isoforms and accumulation of OGT at the immunological synapse of murine T cells. Using a glycoproteomics approach, we identified >200 O-GlcNAc proteins in human T cells. Many of the identified proteins had a functional relationship to RNA metabolism, and consistent with a connection between O-GlcNAc and RNA, inhibition of OGT impaired nascent RNA synthesis upon T cell activation. Overall, our studies provide a global analysis of O-GlcNAc dynamics during T cell activation and the first characterization, to our knowledge, of the O-GlcNAc glycoproteome in human T cells.
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Affiliation(s)
- Peder J Lund
- Interdepartmental Program in Immunology, Stanford University, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305; .,Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA 94305; and.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
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79
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A novel mass spectrometric strategy "BEMAP" reveals Extensive O-linked protein glycosylation in Enterotoxigenic Escherichia coli. Sci Rep 2016; 6:32016. [PMID: 27562176 PMCID: PMC5000012 DOI: 10.1038/srep32016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/01/2016] [Indexed: 11/24/2022] Open
Abstract
The attachment of sugars to proteins via side-chain oxygen atoms (O-linked glycosylation) is seen in all three domains of life. However, a lack of widely-applicable analytical tools has restricted the study of this process, particularly in bacteria. In E. coli, only four O-linked glycoproteins have previously been characterized. Here we present a glycoproteomics technique, termed BEMAP, which is based on the beta-elimination of O-linked glycans followed by Michael-addition of a phosphonic acid derivative, and subsequent titanium dioxide enrichment. This strategy allows site-specific mass-spectrometric identification of proteins with O-linked glycan modifications in a complex biological sample. Using BEMAP we identified cell surface-associated and membrane vesicle glycoproteins from Enterotoxigenic E. coli (ETEC) and non-pathogenic E. coli K-12. We identified 618 glycosylated Serine and Threonine residues mapping to 140 proteins in ETEC, including several known virulence factors, and 34 in E. coli K-12. The two strains had 32 glycoproteins in common. Remarkably, the majority of the ETEC glycoproteins were conserved in both strains but nevertheless were only glycosylated in the pathogen. Therefore, bacterial O-linked glycosylation is much more extensive than previously thought, and is especially important to the pathogen.
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80
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Wani WY, Chatham JC, Darley-Usmar V, McMahon LL, Zhang J. O-GlcNAcylation and neurodegeneration. Brain Res Bull 2016; 133:80-87. [PMID: 27497832 DOI: 10.1016/j.brainresbull.2016.08.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022]
Abstract
O-GlcNAcylation is a dynamic form of protein glycosylation which involves the addition of β-d-N-acetylglucosamine (GlcNAc) via an O-linkage to serine or threonine residues of nuclear, cytoplasmic, mitochondrial and transmembrane proteins. The two enzymes responsible for O-GlcNAc cycling are O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA); their expression and activities in brain are age dependent. More than 1000 O-GlcNAc protein targets have been identified which play critical roles in many cellular processes. In mammalian brain, O-GlcNAc modification of Tau decreases its phosphorylation and toxicity, suggesting a neuroprotective role of pharmacological elevation of brain O-GlcNAc for Alzheimer's disease treatment. Other observations suggest that elevating O-GlcNAc levels may decrease protein clearance or induce apoptosis. This review highlights some of the key findings regarding O-GlcNAcylation in models of neurodegenerative diseases.
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Affiliation(s)
- Willayat Y Wani
- Center for Free Radical Biology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States; Department of Pathology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States
| | - John C Chatham
- Center for Free Radical Biology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States; Department of Pathology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States
| | - Victor Darley-Usmar
- Center for Free Radical Biology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States; Department of Pathology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States
| | - Lori L McMahon
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham,United States
| | - Jianhua Zhang
- Center for Free Radical Biology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States; Department of Pathology, Developmental and Integrative Biology, University of Alabama at Birmingham, United States; Department of Veterans Affairs, Birmingham VA Medical Center, United States.
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81
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Ma J, Banerjee P, Whelan SA, Liu T, Wei AC, Genaro Ramirez-Correa, McComb ME, Costello CE, O’Rourke B, Murphy A, Hart GW. Comparative Proteomics Reveals Dysregulated Mitochondrial O-GlcNAcylation in Diabetic Hearts. J Proteome Res 2016; 15:2254-64. [PMID: 27213235 PMCID: PMC7814404 DOI: 10.1021/acs.jproteome.6b00250] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc), a post-translational modification on serine and threonine residues of many proteins, plays crucial regulatory roles in diverse biological events. As a nutrient sensor, O-GlcNAc modification (O-GlcNAcylation) on nuclear and cytoplasmic proteins underlies the pathology of diabetic complications including cardiomyopathy. However, mitochondrial O-GlcNAcylation, especially in response to chronic hyperglycemia in diabetes, has been poorly explored. We performed a comparative O-GlcNAc profiling of mitochondria from control and streptozotocin (STZ)-induced diabetic rat hearts by using an improved β-elimination/Michael addition with isotopic DTT reagents (BEMAD) followed by tandem mass spectrometric analysis. In total, 86 mitochondrial proteins, involved in diverse pathways, were O-GlcNAcylated. Among them, many proteins have site-specific alterations in O-GlcNAcylation in response to diabetes, which suggests that protein O-GlcNAcylation is a novel layer of regulation mediating adaptive changes in mitochondrial metabolism during the progression of diabetic cardiomyopathy.
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Affiliation(s)
- Junfeng Ma
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Partha Banerjee
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Stephen A. Whelan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Ting Liu
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - An-Chi Wei
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Genaro Ramirez-Correa
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Mark E. McComb
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E. Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Brian O’Rourke
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anne Murphy
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Gerald W. Hart
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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82
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Dong Y, Shahid-Salles S, Sherling D, Fechheimer N, Iyer N, Wells L, Fechheimer M, Furukawa R. De novo actin polymerization is required for model Hirano body formation in Dictyostelium. Biol Open 2016; 5:807-18. [PMID: 27215322 PMCID: PMC4920178 DOI: 10.1242/bio.014944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hirano bodies are eosinophilic, actin-rich inclusions found in autopsied brains in numerous neurodegenerative diseases. The mechanism of Hirano body formation is unknown. Mass spectrometry analysis was performed to identify proteins from partially purified model Hirano bodies from Dictyostelium This analysis identified proteins primarily belonging to ribosomes, proteasomes, mitochondria and cytoskeleton. Profilin, Arp/2/3 and WASH identified by mass spectrometry were found to colocalise with model Hirano bodies. Due to their roles in actin regulation, we selected these proteins for further investigation. Inhibition of the Arp2/3 complex by CK666 prevented formation of model Hirano bodies. Since Arp2/3 activation occurs via the WASH or WAVE complex, we next investigated how these proteins affect Hirano body formation. Whereas model Hirano bodies could form in WASH-deficient cells, they failed to form in cells lacking HSPC300, a member of the WAVE complex. We identified other proteins required for Hirano body formation that include profilin and VASP, an actin nucleation factor. In the case of VASP, both its G- and F-actin binding domains were required for model Hirano body formation. Collectively, our results indicate that de novo actin polymerization is required to form model Hirano bodies.
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Affiliation(s)
- Yun Dong
- Department of Cellular Biology, University of Georgia, Athens, GA, USA 30602
| | | | - Dan Sherling
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA 30602
| | - Nathan Fechheimer
- Department of Cellular Biology, University of Georgia, Athens, GA, USA 30602
| | - Nathan Iyer
- Department of Cellular Biology, University of Georgia, Athens, GA, USA 30602
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA 30602
| | - Marcus Fechheimer
- Department of Cellular Biology, University of Georgia, Athens, GA, USA 30602
| | - Ruth Furukawa
- Department of Cellular Biology, University of Georgia, Athens, GA, USA 30602
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83
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Saito F, Sakamoto I, Kanatani A, Chiba Y. Manganese ion concentration affects production of human core 3 O-glycan in Saccharomyces cerevisiae. Biochim Biophys Acta Gen Subj 2016; 1860:1809-20. [PMID: 27259834 DOI: 10.1016/j.bbagen.2016.05.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/23/2016] [Accepted: 05/28/2016] [Indexed: 01/25/2023]
Abstract
BACKGROUND Production of various mucin-like glycoproteins could be useful for development of antibodies specific to disease-related glycoproteins as well as for the biosynthesis of clinically useful glycoproteins. A Saccharomyces cerevisiae strain capable of in vivo production of mucin-type core 1 structure (Galβ1-3GalNAcα1-O-Ser/Thr) has been reported, but a strain producing core 3 structure (GlcNAcβ1-3GalNAcα1-O-Ser/Thr) has not been constructed. METHODS To generate core 3-producing strain, genes encoding uridine diphosphate (UDP)-Gal-4-epimerase, UDP-GalNAc transporter, UDP-GlcNAc transporter, and two glycosyltransferases were integrated into the genome. A Mucin-1-derived acceptor peptide (MUC1ap) was expressed as an acceptor. The amount of the resulting modified peptide was analyzed by HPLC. RESULTS Introduction of a codon-optimized UDP-GlcNAc:βGal β-1,3-N-acetylglucosaminyltransferase 6 (β3Gn-T6) gene yielded increases in β3Gn-T6 activity but did not alter the level of core 3 production. The highest in vitro activity of β3Gn-T6 was observed at Mn(2+) concentrations of 10mM and above. Supplementation of MnCl2 to the culture medium yielded increases of up to 25% in the accumulation of core 3 on the MUC1ap. The yeast invertase from the core 3-producing strain was less extensively N-glycosylated; however, it was partially restored by the addition of MnCl2 to the medium. CONCLUSIONS Physiological Mn(2+) concentration in S. cerevisiae was insufficient to facilitate optimal synthesis of core 3. Mn(2+) supplementation led to up-regulation of reaction of glycosylation in the Golgi, resulting in increases of core 3 production. GENERAL SIGNIFICANCE This study reveals that control of Mn(2+) concentration is important for production of specific mammalian-type glycans in S. cerevisiae.
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Affiliation(s)
- Fumie Saito
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; GlycoGene Inc., Avenue Takanawa Rm. 412, 3-25-27, Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Izumi Sakamoto
- AcroScale Inc., 3-8-1 Kokubun-cho, Aoba-ku, Sendai, Miyagi 980-0803, Japan
| | - Akio Kanatani
- GlycoGene Inc., Avenue Takanawa Rm. 412, 3-25-27, Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Yasunori Chiba
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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84
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Nika H, Angeletti RH, Hawke DH. Phosphopeptide Enrichment by Covalent Chromatography After Solid Phase Derivatization of Protein Digests on Reversed Phase Supports. Methods Mol Biol 2016; 1355:31-50. [PMID: 26584917 DOI: 10.1007/978-1-4939-3049-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The isolation of the phosphopeptide constituents from phosphoprotein digests is prerequisite to facilitate the mass spectrometric characterization of phosphorylation events. Here, we describe a chemical proteomics approach which combines solid phase derivatization of phosphoprotein digests with phosphopeptide enrichment by covalent chromatography. The use of the solid phase support for derivatization ensures for speed and completeness of reactions. The isolates proved highly suitable for mapping of the sites of phosphorylation by collisionally induced dissociation (CID). The method combines robustness with simplicity of operation using equipment available in biological laboratories, and may be readily extended to map the sites of O-glycosylation.
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Affiliation(s)
- Heinz Nika
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
- Department for Molecular and Developmental Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Ruth Hogue Angeletti
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
- Department for Molecular and Developmental Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - David H Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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85
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Kodiha M, Mahboubi H, Maysinger D, Stochaj U. Gold Nanoparticles Impinge on Nucleoli and the Stress Response in MCF7 Breast Cancer Cells. Nanobiomedicine (Rij) 2016; 3:3. [PMID: 29942378 PMCID: PMC5998265 DOI: 10.5772/62337] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/01/2016] [Indexed: 01/15/2023] Open
Abstract
Cancer cells can take up gold nanoparticles of different morphologies. These particles interact with the plasma membrane and often travel to intracellular organelles. Among organelles, the nucleus is especially susceptible to the damage that is inflicted by gold nanoparticles. Located inside the nucleus, nucleoli are specialized compartments that transcribe ribosomal RNA genes, produce ribosomes and function as cellular stress sensors. Nucleoli are particularly prone to gold nanoparticle-induced injury. As such, small spherical gold nanoparticles and gold nanoflowers interfere with the transcription of ribosomal DNA. However, the underlying mechanisms are not fully understood. In this study, we examined the effects of gold nanoparticles on nucleolar proteins that are critical to ribosome biogenesis and other cellular functions. We show that B23/nucleophosmin, a nucleolar protein that is tightly linked to cancer, is significantly affected by gold nanoparticles. Furthermore, gold nanoparticles impinge on the cellular stress response, as they reduce the abundance of the molecular chaperone hsp70 and O-GlcNAc modified proteins in the nucleus and nucleoli. Together, our studies set the stage for the development of nanomedicines that target the nucleolus to eradicate proliferating cancer cells.
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Affiliation(s)
- Mohamed Kodiha
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Hicham Mahboubi
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Dusica Maysinger
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, QC, Canada
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86
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Steenackers A, Olivier-Van Stichelen S, Baldini SF, Dehennaut V, Toillon RA, Le Bourhis X, El Yazidi-Belkoura I, Lefebvre T. Silencing the Nucleocytoplasmic O-GlcNAc Transferase Reduces Proliferation, Adhesion, and Migration of Cancer and Fetal Human Colon Cell Lines. Front Endocrinol (Lausanne) 2016; 7:46. [PMID: 27252680 PMCID: PMC4879930 DOI: 10.3389/fendo.2016.00046] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
Abstract
The post-translational modification of proteins by O-linked β-N-acetylglucosamine (O-GlcNAc) is regulated by a unique couple of enzymes. O-GlcNAc transferase (OGT) transfers the GlcNAc residue from UDP-GlcNAc, the final product of the hexosamine biosynthetic pathway (HBP), whereas O-GlcNAcase (OGA) removes it. This study and others show that OGT and O-GlcNAcylation levels are increased in cancer cell lines. In that context, we studied the effect of OGT silencing in the colon cancer cell lines HT29 and HCT116 and the primary colon cell line CCD841CoN. Herein, we report that OGT silencing diminished proliferation, in vitro cell survival and adhesion of primary and cancer cell lines. SiOGT dramatically decreased HT29 and CCD841CoN migration, CCD841CoN harboring high capabilities of migration in Boyden chamber system when compared to HT29 and HCT116. The expression levels of actin and tubulin were unaffected by OGT knockdown but siOGT seemed to disorganize microfilament, microtubule, and vinculin networks in CCD841CoN. While cancer cell lines harbor higher levels of OGT and O-GlcNAcylation to fulfill their proliferative and migratory properties, in agreement with their higher consumption of HBP main substrates glucose and glutamine, our data demonstrate that OGT expression is not only necessary for the biological properties of cancer cell lines but also for normal cells.
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Affiliation(s)
- Agata Steenackers
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
| | - Stéphanie Olivier-Van Stichelen
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, USA
| | - Steffi F. Baldini
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
| | - Vanessa Dehennaut
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
- CNRS, UMR 8161, M3T, Mechanisms of Tumorigenesis and Targeted Therapies, «Institut de Biologie de Lille», Pasteur Institute of Lille, FRABio FR 3688, University of Lille, Lille Cedex, France
| | - Robert-Alain Toillon
- U908, CPAC, Cell Plasticity and Cancer, INSERM, University of Lille, Lille, France
| | - Xuefen Le Bourhis
- U908, CPAC, Cell Plasticity and Cancer, INSERM, University of Lille, Lille, France
| | - Ikram El Yazidi-Belkoura
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
| | - Tony Lefebvre
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, FRABio FR 3688, University of Lille, Lille, France
- *Correspondence: Tony Lefebvre,
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87
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Ma J, Liu T, Wei AC, Banerjee P, O'Rourke B, Hart GW. O-GlcNAcomic Profiling Identifies Widespread O-Linked β-N-Acetylglucosamine Modification (O-GlcNAcylation) in Oxidative Phosphorylation System Regulating Cardiac Mitochondrial Function. J Biol Chem 2015; 290:29141-53. [PMID: 26446791 DOI: 10.1074/jbc.m115.691741] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 11/06/2022] Open
Abstract
Dynamic cycling of O-linked β-N-acetylglucosamine (O-GlcNAc) on nucleocytoplasmic proteins serves as a nutrient sensor to regulate numerous biological processes. However, mitochondrial protein O-GlcNAcylation and its effects on function are largely unexplored. In this study, we performed a comparative analysis of the proteome and O-GlcNAcome of cardiac mitochondria from rats acutely (12 h) treated without or with thiamet-G (TMG), a potent and specific inhibitor of O-GlcNAcase. We then determined the functional consequences in mitochondria isolated from the two groups. O-GlcNAcomic profiling finds that over 88 mitochondrial proteins are O-GlcNAcylated, with the oxidative phosphorylation system as a major target. Moreover, in comparison with controls, cardiac mitochondria from TMG-treated rats did not exhibit altered protein abundance but showed overall elevated O-GlcNAcylation of many proteins. However, O-GlcNAc was unexpectedly down-regulated at certain sites of specific proteins. Concomitantly, TMG treatment resulted in significantly increased mitochondrial oxygen consumption rates, ATP production rates, and enhanced threshold for permeability transition pore opening by Ca(2+). Our data reveal widespread and dynamic mitochondrial protein O-GlcNAcylation, serving as a regulator to their function.
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Affiliation(s)
- Junfeng Ma
- From the Department of Biological Chemistry and
| | - Ting Liu
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - An-Chi Wei
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | | | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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88
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Ramirez-Correa GA, Ma J, Slawson C, Zeidan Q, Lugo-Fagundo NS, Xu M, Shen X, Gao WD, Caceres V, Chakir K, DeVine L, Cole RN, Marchionni L, Paolocci N, Hart GW, Murphy AM. Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle. Diabetes 2015; 64:3573-87. [PMID: 26109417 PMCID: PMC4587639 DOI: 10.2337/db14-1107] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 05/14/2015] [Indexed: 11/13/2022]
Abstract
Contractile dysfunction and increased deposition of O-linked β-N-acetyl-d-glucosamine (O-GlcNAc) in cardiac proteins are a hallmark of the diabetic heart. However, whether and how this posttranslational alteration contributes to lower cardiac function remains unclear. Using a refined β-elimination/Michael addition with tandem mass tags (TMT)-labeling proteomic technique, we show that CpOGA, a bacterial analog of O-GlcNAcase (OGA) that cleaves O-GlcNAc in vivo, removes site-specific O-GlcNAcylation from myofilaments, restoring Ca(2+) sensitivity in streptozotocin (STZ) diabetic cardiac muscles. We report that in control rat hearts, O-GlcNAc and O-GlcNAc transferase (OGT) are mainly localized at the Z-line, whereas OGA is at the A-band. Conversely, in diabetic hearts O-GlcNAc levels are increased and OGT and OGA delocalized. Consistent changes were found in human diabetic hearts. STZ diabetic hearts display increased physical interactions of OGA with α-actin, tropomyosin, and myosin light chain 1, along with reduced OGT and increased OGA activities. Our study is the first to reveal that specific removal of O-GlcNAcylation restores myofilament response to Ca(2+) in diabetic hearts and that altered O-GlcNAcylation is due to the subcellular redistribution of OGT and OGA rather than to changes in their overall activities. Thus, preventing sarcomeric OGT and OGA displacement represents a new possible strategy for treating diabetic cardiomyopathy.
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Affiliation(s)
- Genaro A Ramirez-Correa
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Junfeng Ma
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Chad Slawson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS
| | - Quira Zeidan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nahyr S Lugo-Fagundo
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mingguo Xu
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiaoxu Shen
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Wei Dong Gao
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Viviane Caceres
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Khalid Chakir
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lauren DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Robert N Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nazareno Paolocci
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anne M Murphy
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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89
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Pathak S, Alonso J, Schimpl M, Rafie K, Blair DE, Borodkin VS, Albarbarawi O, van Aalten DMF. The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nat Struct Mol Biol 2015; 22:744-750. [PMID: 26237509 PMCID: PMC4979681 DOI: 10.1038/nsmb.3063] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/06/2015] [Indexed: 12/29/2022]
Abstract
O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoans. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay to a library of peptides. We mapped sites of O-GlcNAc modification by electron transfer dissociation MS and found that they correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with Homo sapiens OGT suggest that a combination of size and conformational restriction defines sequence specificity in the -3 to +2 subsites. This work reveals that although the N-terminal TPR repeats of OGT may have roles in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a substantial contribution to O-GlcNAc site specificity.
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Affiliation(s)
- Shalini Pathak
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Jana Alonso
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Marianne Schimpl
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Karim Rafie
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - David E. Blair
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Vladimir S. Borodkin
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Osama Albarbarawi
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M. F. van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK
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90
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Abstract
O-GlcNAcylation is a dynamic protein post-translational modification of serine or threonine residues by an O-linked monosaccharide N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation was discovered three decades ago and its significance has been implicated in several disease states, such as metabolic diseases, cancer and neurological diseases. Yet it remains technically challenging to characterize comprehensively and quantitatively because of its low abundance, low stoichiometry and extremely labile nature under conventional collision-induced dissociation tandem MS conditions. Herein, we review the recent advances addressing these challenges in developing proteomic approaches for site-specific O-GlcNAcylation analysis, including specific enrichment of O-GlcNAc peptides/proteins, unambiguous site-determination of O-GlcNAc modification and quantitative analysis of O-GlcNAcylation.
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91
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Maury JJP, EL Farran CA, Ng D, Loh YH, Bi X, Bardor M, Choo ABH. RING1B O-GlcNAcylation regulates gene targeting of polycomb repressive complex 1 in human embryonic stem cells. Stem Cell Res 2015; 15:182-9. [DOI: 10.1016/j.scr.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/25/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022] Open
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92
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Kim EJ. The Utilities of Chemical Reactions and Molecular Tools for O-GlcNAc Proteomic Studies. Chembiochem 2015; 16:1397-409. [PMID: 26096757 DOI: 10.1002/cbic.201500183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 11/05/2022]
Abstract
The post-translational modification of nuclear and cytoplasmic proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) is involved in a wide variety of cellular processes and is associated with the pathological progression of chronic diseases. Considering its emerging biological significance, systematic identification, site mapping, and quantification of O-GlcNAc proteins are essential and have led to the development of several approaches for O-GlcNAc protein profiling. This minireview mainly focuses on the various useful chemical reactions and molecular tools with detailed reaction mechanisms widely adopted for O-GlcNAc protein/peptide enrichment and its quantification for comprehensive O-GlcNAc protein profiling.
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Affiliation(s)
- Eun Ju Kim
- Department of Science Education-Chemistry Major, Daegu University, Gyeongsan-si, GyeongBuk 712-714 (Republic of Korea). ,
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93
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Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CVC, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. RNA (NEW YORK, N.Y.) 2015; 21:1147-58. [PMID: 25904135 PMCID: PMC4436667 DOI: 10.1261/rna.049130.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5' ends (8-nt repeat-derived 5' tag sequences) but heterogeneous 3' ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3' end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
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Affiliation(s)
- Sonali Majumdar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Neil T Pfister
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Mark Compton
- Department of Poultry Science, University of Georgia, Athens, Georgia 30602, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Claiborne V C Glover
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA Department of Genetics, University of Georgia, Athens, Georgia 30602, USA Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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94
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Tsumoto H, Ogasawara D, Hashii N, Suzuki T, Akimoto Y, Endo T, Miura Y. Enrichment of O-GlcNAc-modified peptides using novel thiol-alkyne and thiol-disulfide exchange. Bioorg Med Chem Lett 2015; 25:2645-9. [PMID: 25980911 DOI: 10.1016/j.bmcl.2015.04.082] [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: 03/30/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 11/29/2022]
Abstract
We have developed a selective method for the enrichment of O-linked β-N-acetylglucosamine (O-GlcNAc)-modified peptides, which uses a newly synthesized thiol-alkyne and a thiol-disulfide exchange. First, O-GlcNAc-modified peptides were enzymatically labeled with an azide-containing GalNAc analog. Then, the azide moiety was reacted with thiol-alkyne through a copper(I)-catalyzed azide-alkyne cycloaddition. The thiol-modified peptides were enriched with thiol-reactive resin through a thiol-disulfide exchange. At least 500fmol of O-GlcNAc-modified peptides was selectively isolated from α-crystallin tryptic peptides and detected by mass spectrometry. This novel enrichment strategy could be used for O-GlcNAcome analysis of biological samples.
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Affiliation(s)
- Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Daisuke Ogasawara
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yoshihiro Akimoto
- Department of Anatomy, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Tamao Endo
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan.
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95
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A critical perspective of the diverse roles of O-GlcNAc transferase in chromatin. Chromosoma 2015; 124:429-42. [PMID: 25894967 PMCID: PMC4666902 DOI: 10.1007/s00412-015-0513-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 02/06/2023]
Abstract
O-linked β-N-Acetylglucosamine (O-GlcNAc) is a posttranslational modification that is catalyzed by O-GlcNAc transferase (Ogt) and found on a plethora of nuclear and cytosolic proteins in animals and plants. Studies in different model organisms revealed that while O-GlcNAc is required for selected processes in Caenorhabditis elegans and Drosophila, it has evolved to become required for cell viability in mice, and this has challenged investigations to identify cellular functions that critically require this modification in mammals. Nevertheless, a principal cellular process that engages O-GlcNAcylation in all of these species is the regulation of gene transcription. Here, we revisit several of the primary experimental observations that led to current models of how O-GlcNAcylation affects gene expression. In particular, we discuss the role of the stable association of Ogt with the transcription factors Hcf1 and Tet, the two main Ogt-interacting proteins in nuclei of mammalian cells. We also critically evaluate the evidence that specific residues on core histones, including serine 112 of histone 2B (H2B-S112), are O-GlcNAcylated in vivo and discuss possible physiological effects of these modifications. Finally, we review our understanding of the role of O-GlcNAcylation in Drosophila, where recent studies suggest that the developmental defects in Ogt mutants are all caused by lack of O-GlcNAcylation of a single transcriptional regulator, the Polycomb repressor protein Polyhomeotic (Ph). Collectively, this reexamination of the experimental evidence suggests that a number of recently propagated models about the role of O-GlcNAcylation in transcriptional control should be treated cautiously.
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96
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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97
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Ahn YH, Kim JY, Yoo JS. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods. MASS SPECTROMETRY REVIEWS 2015; 34:148-65. [PMID: 24889823 PMCID: PMC4340049 DOI: 10.1002/mas.21428] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/20/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.
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Affiliation(s)
- Yeong Hee Ahn
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
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98
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Vercoutter-Edouart AS, El Yazidi-Belkoura I, Guinez C, Baldini S, Leturcq M, Mortuaire M, Mir AM, Steenackers A, Dehennaut V, Pierce A, Lefebvre T. Detection and identification ofO-GlcNAcylated proteins by proteomic approaches. Proteomics 2015; 15:1039-50. [DOI: 10.1002/pmic.201400326] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Céline Guinez
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Steffi Baldini
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Maïté Leturcq
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Marlène Mortuaire
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Anne-Marie Mir
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Agata Steenackers
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Vanessa Dehennaut
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Annick Pierce
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
| | - Tony Lefebvre
- Unit of Structural and Functional Glycobiology; University of Lille 1; Villeneuve d'Ascq France
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99
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Zhang Y, Zhang C, Jiang H, Yang P, Lu H. Fishing the PTM proteome with chemical approaches using functional solid phases. Chem Soc Rev 2015; 44:8260-87. [DOI: 10.1039/c4cs00529e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently available chemical approaches for the enrichment and separation of a PTM proteome using functional solid phases were reviewed.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| | - Cheng Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Hucong Jiang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
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100
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Zuhl M, Dokladny K, Mermier C, Schneider S, Salgado R, Moseley P. The effects of acute oral glutamine supplementation on exercise-induced gastrointestinal permeability and heat shock protein expression in peripheral blood mononuclear cells. Cell Stress Chaperones 2015; 20:85-93. [PMID: 25062931 PMCID: PMC4255255 DOI: 10.1007/s12192-014-0528-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/25/2014] [Accepted: 07/14/2014] [Indexed: 02/04/2023] Open
Abstract
Chronic glutamine supplementation reduces exercise-induced intestinal permeability and inhibits the NF-κB pro-inflammatory pathway in human peripheral blood mononuclear cells. These effects were correlated with activation of HSP70. The purpose of this paper is to test if an acute dose of oral glutamine prior to exercise reduces intestinal permeability along with activation of the heat shock response leading to inhibition of pro-inflammatory markers. Physically active subjects (N = 7) completed baseline and exercise intestinal permeability tests, determined by the percent ratio of urinary lactulose (5 g) to rhamnose (2 g). Exercise included two 60-min treadmill runs at 70 % of VO2max at 30 °C after ingestion of glutamine (Gln) or placebo (Pla). Plasma levels of endotoxin and TNF-α, along with peripheral blood mononuclear cell (PBMC) protein expression of HSP70 and IκBα, were measured pre- and post-exercise and 2 and 4 h post-exercise. Permeability increased in the Pla trial compared to that at rest (0.06 ± 0.01 vs. 0.02 ± 0.018) and did not increase in the Gln trial. Plasma endotoxin was lower at the 4-h time point in the Gln vs. 4 h in the Pla (6.715 ± 0.046 pg/ml vs. 7.952 ± 1.11 pg/ml). TNF-α was lower 4 h post-exercise in the Gln vs. Pla (1.64 ± 0.09 pg/ml vs. 1.87 ± 0.12 pg/ml). PBMC expression of IkBα was higher 4 h post-exercise in the Gln vs. 4 h in the Pla (1.29 ± 0.43 vs. 0.8892 ± 0.040). HSP70 was higher pre-exercise and 2 h post-exercise in the Gln vs. Pla (1.35 ± 0.21 vs. 1.000 ± 0.000 and 1.65 ± 0.21 vs. 1.27 ± 0.40). Acute oral glutamine supplementation prevents an exercise-induced rise in intestinal permeability and suppresses NF-κB activation in peripheral blood mononuclear cells.
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Affiliation(s)
- Micah Zuhl
- Department of Health, Exercise, and Sport Science, University of New Mexico, Albuquerque, NM, 87131, USA,
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