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Hou C, Li W, Li Y, Ma J. O-GlcNAc informatics: advances and trends. Anal Bioanal Chem 2024:10.1007/s00216-024-05531-2. [PMID: 39294469 DOI: 10.1007/s00216-024-05531-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
As a post-translational modification, protein glycosylation is critical in health and disease. O-Linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), as an intracellular monosaccharide modification on proteins, was discovered 40 years ago. Thanks to technological advances, the physiological and pathological significance of O-GlcNAcylation has been gradually revealed and widely appreciated, especially in recent years. O-GlcNAc informatics has been quickly evolving. Clearly, O-GlcNAc informatics tools have not only facilitated O-GlcNAc functional studies, but also provided us a unique perspective on protein O-GlcNAcylation. In this article, we review O-GlcNAc-focused software tools and servers that have been developed for O-GlcNAc research over the past four decades. Specifically, we will (1) survey bioinformatics tools that have facilitated O-GlcNAc proteomics data analysis, (2) introduce databases/servers for O-GlcNAc proteins/sites that have been experimentally identified by individual research labs, (3) describe software tools that have been developed to predict O-GlcNAc sites, and (4) introduce platforms cataloging proteins that interact with the O-GlcNAc cycling enzymes (i.e., O-GlcNAc transferase and O-GlcNAcase). We hope these resources will provide useful information to both experienced researchers and new incomers to the O-GlcNAc field. We anticipate that this review provides a framework to stimulate the future development of more sophisticated informatic tools for O-GlcNAc research.
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Affiliation(s)
- Chunyan Hou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Weiyu Li
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20007, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yaoxiang Li
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20007, USA.
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2
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Potter SC, Gibbs BE, Hammel FA, Joiner CM, Paulo JA, Janetzko J, Levine ZG, Fei GQ, Haggarty SJ, Walker S. Dissecting OGT's TPR domain to identify determinants of cellular function. Proc Natl Acad Sci U S A 2024; 121:e2401729121. [PMID: 38768345 PMCID: PMC11145291 DOI: 10.1073/pnas.2401729121] [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] [Received: 02/03/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
O-GlcNAc transferase (OGT) is an essential mammalian enzyme that glycosylates myriad intracellular proteins and cleaves the transcriptional coregulator Host Cell Factor 1 to regulate cell cycle processes. Via these catalytic activities as well as noncatalytic protein-protein interactions, OGT maintains cell homeostasis. OGT's tetratricopeptide repeat (TPR) domain is important in substrate recognition, but there is little information on how changing the TPR domain impacts its cellular functions. Here, we investigate how altering OGT's TPR domain impacts cell growth after the endogenous enzyme is deleted. We find that disrupting the TPR residues required for OGT dimerization leads to faster cell growth, whereas truncating the TPR domain slows cell growth. We also find that OGT requires eight of its 13 TPRs to sustain cell viability. OGT-8, like the nonviable shorter OGT variants, is mislocalized and has reduced Ser/Thr glycosylation activity; moreover, its interactions with most of wild-type OGT's binding partners are broadly attenuated. Therefore, although OGT's five N-terminal TPRs are not essential for cell viability, they are required for proper subcellular localization and for mediating many of OGT's protein-protein interactions. Because the viable OGT truncation variant we have identified preserves OGT's essential functions, it may facilitate their identification.
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Affiliation(s)
- Sarah C. Potter
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | - Bettine E. Gibbs
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - Forrest A. Hammel
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - Cassandra M. Joiner
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - Joao A. Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - John Janetzko
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Zebulon G. Levine
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - George Q. Fei
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute of Harvard Medical School, Boston, MA02115
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3
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Chen Q, Xu X, Xie S, Sheng A, Han N, Tian Z, Wang X, Li F, Linhardt RJ, Zhang F, Jin L, Zhang Q, Chi L. Improving impact of heparan sulfate on the endothelial glycocalyx abnormalities in atherosclerosis as revealed by glycan-protein interactome. Carbohydr Polym 2024; 330:121834. [PMID: 38368111 DOI: 10.1016/j.carbpol.2024.121834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
Endothelial dysfunction induced by oxidative stress is an early predictor of atherosclerosis, which can cause various cardiovascular diseases. The glycocalyx layer on the endothelial cell surface acts as a barrier to maintain endothelial biological function, and it can be impaired by oxidative stress. However, the mechanism of glycocalyx damage during the development of atherosclerosis remains largely unclear. Herein, we established a novel strategy to address these issues from the glycomic perspective that has long been neglected. Using countercharged fluorescence protein staining and quantitative mass spectrometry, we found that heparan sulfate, a major component of the glycocalyx, was structurally altered by oxidative stress. Comparative proteomics and protein microarray analysis revealed several new heparan sulfate-binding proteins, among which alpha-2-Heremans-Schmid glycoprotein (AHSG) was identified as a critical protein. The molecular mechanism of AHSG with heparin was characterized through several methods. A heparan analog could relieve atherosclerosis by protecting heparan sulfate from degradation during oxidative stress and by reducing the accumulation of AHSG at lesion sites. In the present study, the molecular mechanism of anti-atherosclerotic effect of heparin through interaction with AHSG was revealed. These findings provide new insights into understanding of glycocalyx damage in atherosclerosis and lead to the development of corresponding therapeutics.
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Affiliation(s)
- Qingqing Chen
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaohui Xu
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Shaoshuai Xie
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Anran Sheng
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Naihan Han
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Zhenyu Tian
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Xiaowei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Fuchuan Li
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Lan Jin
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China.
| | - Qunye Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Qilu Hospital, Shandong University, Jinan, Shandong 250021, China.
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China.
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Dupas T, Lauzier B, McGraw S. O-GlcNAcylation: the sweet side of epigenetics. Epigenetics Chromatin 2023; 16:49. [PMID: 38093337 PMCID: PMC10720106 DOI: 10.1186/s13072-023-00523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Histones display a wide variety of post-translational modifications, including acetylation, methylation, and phosphorylation. These epigenetic modifications can influence chromatin structure and function without altering the DNA sequence. Histones can also undergo post-translational O-GlcNAcylation, a rather understudied modification that plays critical roles in almost all biological processes and is added and removed by O-linked N-acetylglucosamine transferase and O-GlcNAcase, respectively. This review provides a current overview of our knowledge of how O-GlcNAcylation impacts the histone code both directly and by regulating other chromatin modifying enzymes. This highlights the pivotal emerging role of O-GlcNAcylation as an essential epigenetic marker.
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Affiliation(s)
- Thomas Dupas
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Canada.
- Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
| | - Benjamin Lauzier
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Canada
- Nantes Université, CNRS, INSERM, L'institut du Thorax, 44000, Nantes, France
| | - Serge McGraw
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Canada.
- Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard‑Montpetit, Montréal, QC, H3T 1J4, Canada.
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Griffin ME, Thompson JW, Xiao Y, Sweredoski MJ, Aksenfeld RB, Jensen EH, Koldobskaya Y, Schacht AL, Kim TD, Choudhry P, Lomenick B, Garbis SD, Moradian A, Hsieh-Wilson LC. Functional glycoproteomics by integrated network assembly and partitioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.541482. [PMID: 37398272 PMCID: PMC10312638 DOI: 10.1101/2023.06.13.541482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.
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Affiliation(s)
- Matthew E. Griffin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - John W. Thompson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Yao Xiao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rita B. Aksenfeld
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth H. Jensen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yelena Koldobskaya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew L. Schacht
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Terry D. Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Priya Choudhry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Spiros D. Garbis
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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6
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Ben Ahmed A, Lemaire Q, Scache J, Mariller C, Lefebvre T, Vercoutter-Edouart AS. O-GlcNAc Dynamics: The Sweet Side of Protein Trafficking Regulation in Mammalian Cells. Cells 2023; 12:1396. [PMID: 37408229 PMCID: PMC10216988 DOI: 10.3390/cells12101396] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 07/07/2023] Open
Abstract
The transport of proteins between the different cellular compartments and the cell surface is governed by the secretory pathway. Alternatively, unconventional secretion pathways have been described in mammalian cells, especially through multivesicular bodies and exosomes. These highly sophisticated biological processes rely on a wide variety of signaling and regulatory proteins that act sequentially and in a well-orchestrated manner to ensure the proper delivery of cargoes to their final destination. By modifying numerous proteins involved in the regulation of vesicular trafficking, post-translational modifications (PTMs) participate in the tight regulation of cargo transport in response to extracellular stimuli such as nutrient availability and stress. Among the PTMs, O-GlcNAcylation is the reversible addition of a single N-acetylglucosamine monosaccharide (GlcNAc) on serine or threonine residues of cytosolic, nuclear, and mitochondrial proteins. O-GlcNAc cycling is mediated by a single couple of enzymes: the O-GlcNAc transferase (OGT) which catalyzes the addition of O-GlcNAc onto proteins, and the O-GlcNAcase (OGA) which hydrolyses it. Here, we review the current knowledge on the emerging role of O-GlcNAc modification in the regulation of protein trafficking in mammalian cells, in classical and unconventional secretory pathways.
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Hu CW, Xie J, Jiang J. The Emerging Roles of Protein Interactions with O-GlcNAc Cycling Enzymes in Cancer. Cancers (Basel) 2022; 14:5135. [PMID: 36291918 PMCID: PMC9600386 DOI: 10.3390/cancers14205135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 09/11/2023] Open
Abstract
The dynamic O-GlcNAc modification of intracellular proteins is an important nutrient sensor for integrating metabolic signals into vast networks of highly coordinated cellular activities. Dysregulation of the sole enzymes responsible for O-GlcNAc cycling, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), and the associated cellular O-GlcNAc profile is a common feature across nearly every cancer type. Many studies have investigated the effects of aberrant OGT/OGA expression on global O-GlcNAcylation activity in cancer cells. However, recent studies have begun to elucidate the roles of protein-protein interactions (PPIs), potentially through regions outside of the immediate catalytic site of OGT/OGA, that regulate greater protein networks to facilitate substrate-specific modification, protein translocalization, and the assembly of larger biomolecular complexes. Perturbation of OGT/OGA PPI networks makes profound changes in the cell and may directly contribute to cancer malignancies. Herein, we highlight recent studies on the structural features of OGT and OGA, as well as the emerging roles and molecular mechanisms of their aberrant PPIs in rewiring cancer networks. By integrating complementary approaches, the research in this area will aid in the identification of key protein contacts and functional modules derived from OGT/OGA that drive oncogenesis and will illuminate new directions for anti-cancer drug development.
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Affiliation(s)
| | | | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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Xu B, Zhang C, Jiang A, Zhang X, Liang F, Wang X, Li D, Liu C, Liu X, Xia J, Li Y, Wang Y, Yang Z, Chen J, Zhou Y, Chen L, Sun H. Histone methyltransferase Dot1L recruits O-GlcNAc transferase to target chromatin sites to regulate histone O-GlcNAcylation. J Biol Chem 2022; 298:102115. [PMID: 35690146 PMCID: PMC9283943 DOI: 10.1016/j.jbc.2022.102115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 11/05/2022] Open
Abstract
O-GlcNAc transferase (OGT) is the distinctive enzyme responsible for catalyzing O-GlcNAc addition to the serine or threonine residues of thousands of cytoplasmic and nuclear proteins involved in such basic cellular processes as DNA damage repair, RNA splicing, and transcription preinitiation and initiation complex assembly. However, the molecular mechanism by which OGT regulates gene transcription remains elusive. Using proximity labeling-based mass spectrometry, here, we searched for functional partners of OGT and identified interacting protein Dot1L, a conserved and unique histone methyltransferase known to mediate histone H3 Lys79 methylation, which is required for gene transcription, DNA damage repair, cell proliferation, and embryo development. Although this specific interaction with OGT does not regulate the enzymatic activity of Dot1L, we show that it does facilitate OGT-dependent histone O-GlcNAcylation. Moreover, we demonstrate that OGT associates with Dot1L at transcription start sites and that depleting Dot1L decreases OGT associated with chromatin globally. Notably, we also show that downregulation of Dot1L reduces the levels of histone H2B S112 O-GlcNAcylation and histone H2B K120 ubiquitination in vivo, which are associated with gene transcription regulation. Taken together, these results reveal that O-GlcNAcylation of chromatin is dependent on Dot1L.
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Affiliation(s)
- Bo Xu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Can Zhang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Ao Jiang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Xianhong Zhang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Fenfei Liang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Xueqing Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Danni Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Chenglong Liu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Xiaomei Liu
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Jing Xia
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Yirong Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Zelan Yang
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Jia Chen
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Yu Zhou
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Liang Chen
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China.
| | - Hui Sun
- College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China; Hubei Province key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430072, Hubei Province, China.
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9
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de Seny D, Baiwir D, Bianchi E, Cobraiville G, Deroyer C, Poulet C, Malaise O, Paulissen G, Kaiser MJ, Hauzeur JP, Mazzucchelli G, Delvenne P, Malaise M. New Proteins Contributing to Immune Cell Infiltration and Pannus Formation of Synovial Membrane from Arthritis Diseases. Int J Mol Sci 2021; 23:ijms23010434. [PMID: 35008858 PMCID: PMC8745719 DOI: 10.3390/ijms23010434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/15/2023] Open
Abstract
An inflamed synovial membrane plays a major role in joint destruction and is characterized by immune cells infiltration and fibroblast proliferation. This proteomic study considers the inflammatory process at the molecular level by analyzing synovial biopsies presenting a histological inflammatory continuum throughout different arthritis joint diseases. Knee synovial biopsies were obtained from osteoarthritis (OA; n = 9), chronic pyrophosphate arthropathy (CPPA; n = 7) or rheumatoid arthritis (RA; n = 8) patients. The histological inflammatory score was determined using a semi-quantitative scale based on synovial hyperplasia, lymphocytes, plasmocytes, neutrophils and macrophages infiltration. Proteomic analysis was performed by liquid chromatography-mass spectrometry (LC-MS/MS). Differentially expressed proteins were confirmed by immunohistochemistry. Out of the 1871 proteins identified and quantified by LC-MS/MS, 10 proteins (LAP3, MANF, LCP1, CTSZ, PTPRC, DNAJB11, EML4, SCARA5, EIF3K, C1orf123) were differentially expressed in the synovial membrane of at least one of the three disease groups (RA, OA and CPPA). Significant increased expression of the seven first proteins was detected in RA and correlated to the histological inflammatory score. Proteomics is therefore a powerful tool that provides a molecular pattern to the classical histology usually applied for synovitis characterization. Except for LCP1, CTSZ and PTPRC, all proteins have never been described in human synovitis.
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Affiliation(s)
- Dominique de Seny
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
- Correspondence: ; Tel.: +32-366-24-74
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liège, 4000 Liège, Belgium; (D.B.); (P.D.)
| | - Elettra Bianchi
- Department of Pathology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium;
| | - Gaël Cobraiville
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Céline Deroyer
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Christophe Poulet
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Olivier Malaise
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Geneviève Paulissen
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Marie-Joëlle Kaiser
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Jean-Philippe Hauzeur
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium;
| | - Philippe Delvenne
- GIGA Proteomics Facility, University of Liège, 4000 Liège, Belgium; (D.B.); (P.D.)
| | - Michel Malaise
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
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10
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Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM. Truncation of the TPR domain of OGT alters substrate and glycosite selection. Anal Bioanal Chem 2021; 413:7385-7399. [PMID: 34725712 DOI: 10.1007/s00216-021-03731-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
O-GlcNAc transferase (OGT) is an essential enzyme that installs O-linked N-acetylglucosamine (O-GlcNAc) to thousands of protein substrates. OGT and its isoforms select from these substrates through the tetratricopeptide repeat (TPR) domain, yet the impact of truncations to the TPR domain on substrate and glycosite selection is unresolved. Here, we report the effects of iterative truncations to the TPR domain of OGT on substrate and glycosite selection with the model protein GFP-JunB and the surrounding O-GlcNAc proteome in U2OS cells. Iterative truncation of the TPR domain of OGT maintains glycosyltransferase activity but alters subcellular localization of OGT in cells. The glycoproteome and glycosites modified by four OGT TPR isoforms were examined on the whole proteome and a single target protein, GFP-JunB. We found the greatest changes in O-GlcNAc on proteins associated with mRNA splicing processes and that the first four TPRs of the canonical nucleocytoplasmic OGT had the broadest substrate scope. Subsequent glycosite analysis revealed that alteration to the last four TPRs corresponded to the greatest shift in the resulting O-GlcNAc consensus sequence. This dataset provides a foundation to analyze how perturbations to the TPR domain and expression of OGT isoforms affect the glycosylation of substrates, which will be critical for future efforts in protein engineering of OGT, the biology of OGT isoforms, and diseases associated with the TPR domain of OGT.
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Affiliation(s)
- Daniel H Ramirez
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alexandria K D'Souza
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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11
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Ma J, Hou C, Li Y, Chen S, Wu C. OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. Int J Mol Sci 2021; 22:ijms22179620. [PMID: 34502531 PMCID: PMC8431785 DOI: 10.3390/ijms22179620] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
Interactions between proteins are essential to any cellular process and constitute the basis for molecular networks that determine the functional state of a cell. With the technical advances in recent years, an astonishingly high number of protein–protein interactions has been revealed. However, the interactome of O-linked N-acetylglucosamine transferase (OGT), the sole enzyme adding the O-linked β-N-acetylglucosamine (O-GlcNAc) onto its target proteins, has been largely undefined. To that end, we collated OGT interaction proteins experimentally identified in the past several decades. Rigorous curation of datasets from public repositories and O-GlcNAc-focused publications led to the identification of up to 929 high-stringency OGT interactors from multiple species studied (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, and others). Among them, 784 human proteins were found to be interactors of human OGT. Moreover, these proteins spanned a very diverse range of functional classes (e.g., DNA repair, RNA metabolism, translational regulation, and cell cycle), with significant enrichment in regulating transcription and (co)translation. Our dataset demonstrates that OGT is likely a hub protein in cells. A webserver OGT-Protein Interaction Network (OGT-PIN) has also been created, which is freely accessible.
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Affiliation(s)
- Junfeng Ma
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
- Correspondence: ; Tel.: +1-202-6873802
| | - Chunyan Hou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Yaoxiang Li
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
| | - Shufu Chen
- School of Engineering, Pennsylvania State University Behrend, Erie, PA 16563, USA;
| | - Ci Wu
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
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12
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Stephen HM, Praissman JL, Wells L. Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability. J Proteome Res 2021; 20:1229-1242. [PMID: 33356293 PMCID: PMC8577549 DOI: 10.1021/acs.jproteome.0c00604] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The O-GlcNAc transferase (OGT) modifies nuclear and cytoplasmic proteins with β-N-acetyl-glucosamine (O-GlcNAc). With thousands of O-GlcNAc-modified proteins but only one OGT encoded in the mammalian genome, a prevailing question is how OGT selects its substrates. Prior work has indicated that the tetratricopeptide repeat (TPR) domain of OGT is involved in substrate selection. Furthermore, several variants of OGT causal for X-linked intellectual disability (XLID) occur in the TPR domain. Therefore, we adapted the BioID labeling method to identify interactors of a TPR-BirA* fusion protein in HeLa cells. We identified 115 interactors representing known and novel O-GlcNAc-modified proteins and OGT interactors (raw data deposited in MassIVE, Dataset ID MSV000085626). The interactors are enriched in known OGT processes (e.g., chromatin remodeling) as well as processes in which OGT has yet to be implicated (e.g., pre-mRNA processing). Importantly, the identified TPR interactors are linked to several disease states but most notably are enriched in pathologies featuring intellectual disability that may underlie the mechanism by which mutations in OGT lead to XLID. This interactome for the TPR domain of OGT serves as a jumping-off point for future research exploring the role of OGT, the TPR domain, and its protein interactors in multiple cellular processes and disease mechanisms, including intellectual disability.
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Affiliation(s)
- Hannah M. Stephen
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, United States of America
| | - Jeremy L. Praissman
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, United States of America
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30605, United States of America
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13
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Stephen HM, Adams TM, Wells L. Regulating the Regulators: Mechanisms of Substrate Selection of the O-GlcNAc Cycling Enzymes OGT and OGA. Glycobiology 2021; 31:724-733. [PMID: 33498085 DOI: 10.1093/glycob/cwab005] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/20/2022] Open
Abstract
Thousands of nuclear and cytosolic proteins are modified with a single β-N-acetylglucosamine on serine and threonine residues in mammals, a modification termed O-GlcNAc. This modification is essential for normal development and plays important roles in virtually all intracellular processes. Additionally, O-GlcNAc is involved in many disease states, including cancer, diabetes, and X-linked intellectual disability. Given the myriad of functions of the O-GlcNAc modification, it is therefore somewhat surprising that O-GlcNAc cycling is mediated by only two enzymes: the O-GlcNAc transferase (OGT), which adds O-GlcNAc, and the O-GlcNAcase (OGA), which removes it. A significant outstanding question in the O-GlcNAc field is how do only two enzymes mediate such an abundant and dynamic modification. In this review, we explore the current understanding of mechanisms for substrate selection for the O-GlcNAc cycling enzymes. These mechanisms include direct substrate interaction with specific domains of OGT or OGA, selection of interactors via partner proteins, posttranslational modification of OGT or OGA, nutrient sensing, and localization alteration. Altogether, current research paints a picture of an exquisitely regulated and complex system by which OGT and OGA select substrates. We also make recommendations for future work, toward the goal of identifying interaction mechanisms for specific substrates that may be able to be exploited for various research and medical treatment goals.
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Affiliation(s)
- Hannah M Stephen
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens 30602, GA, USA
| | - Trevor M Adams
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens 30602, GA, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens 30602, GA, USA
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14
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Ma J, Wu C, Hart GW. Analytical and Biochemical Perspectives of Protein O-GlcNAcylation. Chem Rev 2021; 121:1513-1581. [DOI: 10.1021/acs.chemrev.0c00884] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Gerald W. Hart
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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15
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Luo PM, Boyce M. Directing Traffic: Regulation of COPI Transport by Post-translational Modifications. Front Cell Dev Biol 2019; 7:190. [PMID: 31572722 PMCID: PMC6749011 DOI: 10.3389/fcell.2019.00190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
The coat protein complex I (COPI) is an essential, highly conserved pathway that traffics proteins and lipids between the endoplasmic reticulum (ER) and the Golgi. Many aspects of the COPI machinery are well understood at the structural, biochemical and genetic levels. However, we know much less about how cells dynamically modulate COPI trafficking in response to changing signals, metabolic state, stress or other stimuli. Recently, post-translational modifications (PTMs) have emerged as one common theme in the regulation of the COPI pathway. Here, we review a range of modifications and mechanisms that govern COPI activity in interphase cells and suggest potential future directions to address as-yet unanswered questions.
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Affiliation(s)
- Peter M Luo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
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16
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Xu QG, Yuan SX, Tao QF, Yu J, Cai J, Yang Y, Guo XG, Lin KY, Ma JZ, Dai DS, Wang ZG, Gu FM, Zhao LH, Li LQ, Liu JF, Sun SH, Zang YJ, Liu H, Yang F, Zhou WP. A novel HBx genotype serves as a preoperative predictor and fails to activate the JAK1/STATs pathway in hepatocellular carcinoma. J Hepatol 2019; 70:904-917. [PMID: 30654066 DOI: 10.1016/j.jhep.2019.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 11/29/2018] [Accepted: 01/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Genetic variability in the hepatitis B virus X gene (HBx) is frequently observed and is associated with hepatocellular carcinoma (HCC) progression. However, a genotype classification based on the full-length HBx sequence and the impact of genotypes on hepatitis B virus (HBV)-related HCC prognosis remain unclear. We therefore aimed to perform this genotype classification and assess its clinical impact. METHODS We classified the genotypes of the full-length HBx gene through sequencing and a cluster analysis of HBx DNA from a cohort of patients with HBV-related HCC, which served as the primary cohort (n = 284). Two independent HBV-related HCC cohorts, a validation cohort (n = 171) and a serum cohort (n = 168), were used to verify the results. Protein microarray assay analysis was performed to explore the underlying mechanism. RESULTS In the primary cohort, the HBx DNA was classified into 3 genotypes: HBx-EHBH1, HBx-EHBH2, and HBx-EHBH3. HBx-EHBH2 (HBx-E2) indicated better recurrence-free survival and overall survival for patients with HCC. HBx-E2 was significantly correlated with the absence of liver cirrhosis, a small tumor size, a solitary tumor, complete encapsulation and Barcelona Clinic Liver Cancer (BCLC) stage A-0 tumors. Additionally, HBx-E2 served as a significant prognostic factor for patients with BCLC stage B HCC after hepatectomy. Mechanistically, HBx-E2 is unable to promote proliferation in HCC cells and normal hepatocytes. It also fails to activate the Janus kinase 1 (JAK1)/signal transducer and activator of transcription 3 (STAT3)/STAT5 pathway. CONCLUSION Our study identifies a novel HBx genotype that is unable to promote the proliferation of HCC cells and suggests a potential marker to preoperatively predict the prognosis of patients with BCLC stage B, HBV-associated, HCC. LAY SUMMARY We classified a novel genotype of the full-length hepatitis B virus X gene (HBx), HBx-E2. This genotype was identified in tumor and nontumor tissues from patients with hepatitis B virus-related hepatocellular carcinoma. HBx-E2 could preoperatively predict the prognosis of patients with intermediate stage hepatocellular carcinoma, after resection.
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Affiliation(s)
- Qing-Guo Xu
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China; Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Sheng-Xian Yuan
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Qi-Fei Tao
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jian Yu
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jie Cai
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yuan Yang
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xing-Gang Guo
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Kong-Ying Lin
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China; Mengchao Hepatobiliary Hospital of Fujian Medical University, Fujian, China
| | - Jin-Zhao Ma
- The Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - De-Shu Dai
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Zhen-Guang Wang
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Fang-Ming Gu
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ling-Hao Zhao
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Le-Qun Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Guangxi, China
| | - Jing-Feng Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fujian, China
| | - Shu-Han Sun
- The Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - Yun-Jin Zang
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Liu
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
| | - Fu Yang
- The Department of Medical Genetics, Second Military Medical University, Shanghai, China.
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, China.
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17
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Cao T, Lyu L, Jia H, Wang J, Du F, Pan L, Li Z, Xing A, Xiao J, Ma Y, Zhang Z. A Two-Way Proteome Microarray Strategy to Identify Novel Mycobacterium tuberculosis-Human Interactors. Front Cell Infect Microbiol 2019; 9:65. [PMID: 30984625 PMCID: PMC6448480 DOI: 10.3389/fcimb.2019.00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is still a serious threat to human health which is caused by mycobacterium tuberculosis (Mtb). The main reason for failure to eliminate TB is lack of clearly understanding the molecular mechanism of Mtb pathogenesis. Determining human Mtb-interacting proteins enables us to characterize the mechanism and identify potential molecular targets for TB diagnosis and treatment. However, experimentally systematic Mtb interactors are not readily available. In this study, we performed an unbiased, comprehensive two-way proteome microarray based approach to systematically screen global human Mtb interactors and determine the binding partners of Mtb effectors. Our results, for the first time, screened 84 potential human Mtb interactors. Bioinformatic analysis further highlighted these protein candidates might engage in a wide range of cellular functions such as activation of DNA endogenous promoters, transcription of DNA/RNA and necrosis, as well as immune-related signaling pathways. Then, using Mtb proteome microarray followed His tagged pull-down assay and Co-IP, we identified one interacting partner (Rv0577) for the protein candidate NRF1 and three binding partners (Rv0577, Rv2117, Rv2423) for SMAD2, respectively. This study gives new insights into the profile of global Mtb interactors potentially involved in Mtb pathogenesis and demonstrates a powerful strategy in the discovery of Mtb effectors.
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Affiliation(s)
- Tingming Cao
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lingna Lyu
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinghui Wang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fengjiao Du
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zihui Li
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Aiying Xing
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jing Xiao
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yu Ma
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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18
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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19
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Flores-Martín J, Reyna L, Cruz Del Puerto M, Rojas ML, Panzetta-Dutari GM, Genti-Raimondi S. Hexosamine pathway regulates StarD7 expression in JEG-3 cells. Mol Biol Rep 2018; 45:2593-2600. [PMID: 30315445 DOI: 10.1007/s11033-018-4428-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/05/2018] [Indexed: 11/29/2022]
Abstract
StarD7 is a lipid binding protein involved in the delivery of phosphatidylcholine to the mitochondria whose promoter is activated by Wnt/β-catenin signaling. Although the majority of glucose enters glycolysis, ~ 2-5% of it can be metabolized via the hexosamine biosynthetic pathway (HBP). Considering that HBP has been implicated in the regulation of β-catenin we explored if changes in glucose levels modulate StarD7 expression by the HBP in trophoblast cells. We found an increase in StarD7 as well as in β-catenin expression following high-glucose (25 mM) treatment in JEG-3 cells; these effects were abolished in the presence of HBP inhibitors. Moreover, since HBP is able to promote unfolded protein response (UPR) the protein levels of GRP78, Ire1α, calnexin, p-eIF2α and total eIF2α as well as XBP1 mRNA was measured. Our results indicate that a diminution in glucose concentration leads to a decrease in StarD7 expression and an increase in the UPR markers: GRP78 and Ire1α. Conversely, an increase in glucose is associated to high StarD7 levels and low GRP78 expression, phospho-eIF2α and XBP1 splicing, although Ire1α remains high when cells are restored to high glucose. Taken together these findings indicate that glucose modulates StarD7 and β-catenin expression through the HBP associated to UPR, suggesting the existence of a link between UPR and HBP in trophoblast cells. This is the first study reporting the effects of glucose on StarD7 in trophoblast cells. These data highlight the importance to explore the role of StarD7 in placenta disorders related to nutrient availability.
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Affiliation(s)
- Jésica Flores-Martín
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Luciana Reyna
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Mariano Cruz Del Puerto
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - María L Rojas
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Graciela M Panzetta-Dutari
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Susana Genti-Raimondi
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina. .,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ciudad Universitaria, X5000HUA, Córdoba, Argentina. .,Departamento de Bioquímica Clínica, CIBICI-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, X5000HUA, Córdoba, Argentina.
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20
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A Rahaman SN, Mat Yusop J, Mohamed-Hussein ZA, Aizat WM, Ho KL, Teh AH, Waterman J, Tan BK, Tan HL, Li AY, Chen ES, Ng CL. Crystal structure and functional analysis of human C1ORF123. PeerJ 2018; 6:e5377. [PMID: 30280012 PMCID: PMC6166629 DOI: 10.7717/peerj.5377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
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Affiliation(s)
| | - Jastina Mat Yusop
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.,Center for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, England, United Kingdom
| | - Boon Keat Tan
- Division of Human Biology, School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Hwei Ling Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Adelicia Yongling Li
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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21
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Selvan N, George S, Serajee FJ, Shaw M, Hobson L, Kalscheuer V, Prasad N, Levy SE, Taylor J, Aftimos S, Schwartz CE, Huq AM, Gecz J, Wells L. O-GlcNAc transferase missense mutations linked to X-linked intellectual disability deregulate genes involved in cell fate determination and signaling. J Biol Chem 2018; 293:10810-10824. [PMID: 29769320 DOI: 10.1074/jbc.ra118.002583] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/27/2018] [Indexed: 01/17/2023] Open
Abstract
It is estimated that ∼1% of the world's population has intellectual disability, with males affected more often than females. OGT is an X-linked gene encoding for the enzyme O-GlcNAc transferase (OGT), which carries out the reversible addition of N-acetylglucosamine (GlcNAc) to Ser/Thr residues of its intracellular substrates. Three missense mutations in the tetratricopeptide (TPR) repeats of OGT have recently been reported to cause X-linked intellectual disability (XLID). Here, we report the discovery of two additional novel missense mutations (c.775 G>A, p.A259T, and c.1016 A>G, p.E339G) in the TPR domain of OGT that segregate with XLID in affected families. Characterization of all five of these XLID missense variants of OGT demonstrates modest declines in thermodynamic stability and/or activities of the variants. We engineered each of the mutations into a male human embryonic stem cell line using CRISPR/Cas9. Investigation of the global O-GlcNAc profile as well as OGT and O-GlcNAc hydrolase levels by Western blotting showed no gross changes in steady-state levels in the engineered lines. However, analyses of the differential transcriptomes of the OGT variant-expressing stem cells revealed shared deregulation of genes involved in cell fate determination and liver X receptor/retinoid X receptor signaling, which has been implicated in neuronal development. Thus, here we reveal two additional mutations encoding residues in the TPR regions of OGT that appear causal for XLID and provide evidence that the relatively stable and active TPR variants may share a common, unelucidated mechanism of altering gene expression profiles in human embryonic stem cells.
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Affiliation(s)
- Nithya Selvan
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Stephan George
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Fatema J Serajee
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Marie Shaw
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia
| | - Lynne Hobson
- the Women's and Children's Hospital, North Adelaide, South Australia 5006, Australia
| | - Vera Kalscheuer
- the Research Group Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Nripesh Prasad
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Shawn E Levy
- the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Juliet Taylor
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | - Salim Aftimos
- the Genetic Health Services New Zealand-Northern Hub, Auckland City Hospital, Auckland 1142, New Zealand
| | | | - Ahm M Huq
- the Departments of Pediatrics and of Neurology, Wayne State University, Detroit, Michigan 48201
| | - Jozef Gecz
- the Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide South Australia 5006, Australia.,the South Australian Health and Medical Research Institute, Adelaide, South Australia 5006, Australia
| | - Lance Wells
- From the Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,
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22
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Laarse SAM, Leney AC, Heck AJR. Crosstalk between phosphorylation and O‐Glc
NA
cylation: friend or foe. FEBS J 2018; 285:3152-3167. [DOI: 10.1111/febs.14491] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Saar A. M. Laarse
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
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23
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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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24
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He X, Jiang HW, Chen H, Zhang HN, Liu Y, Xu ZW, Wu FL, Guo SJ, Hou JL, Yang MK, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity. Mol Cell Proteomics 2017; 16:2243-2253. [PMID: 29018126 DOI: 10.1074/mcp.ra117.000296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.
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Affiliation(s)
- Xiang He
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- ¶Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Kun Yang
- ‖Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Yan
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao-Yu Deng
- **State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§§School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Xian-En Zhang
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; .,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,¶¶State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
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25
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Levine ZG, Walker S. The Biochemistry of O-GlcNAc Transferase: Which Functions Make It Essential in Mammalian Cells? Annu Rev Biochem 2017; 85:631-57. [PMID: 27294441 DOI: 10.1146/annurev-biochem-060713-035344] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O-linked N-acetylglucosamine transferase (OGT) is found in all metazoans and plays an important role in development but at the single-cell level is only essential in dividing mammalian cells. Postmitotic mammalian cells and cells of invertebrates such as Caenorhabditis elegans and Drosophila can survive without copies of OGT. Why OGT is required in dividing mammalian cells but not in other cells remains unknown. OGT has multiple biochemical activities. Beyond its well-known role in adding β-O-GlcNAc to serine and threonine residues of nuclear and cytoplasmic proteins, OGT also acts as a protease in the maturation of the cell cycle regulator host cell factor 1 (HCF-1) and serves as an integral member of several protein complexes, many of them linked to gene expression. In this review, we summarize current understanding of the mechanisms underlying OGT's biochemical activities and address whether known functions of OGT could be related to its essential role in dividing mammalian cells.
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Affiliation(s)
- Zebulon G Levine
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115; ,
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26
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System-based proteomic and metabonomic analysis of the Df(16)A +/- mouse identifies potential miR-185 targets and molecular pathway alterations. Mol Psychiatry 2017; 22:384-395. [PMID: 27001617 PMCID: PMC5322275 DOI: 10.1038/mp.2016.27] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 01/24/2016] [Accepted: 01/28/2016] [Indexed: 12/25/2022]
Abstract
Deletions on chromosome 22q11.2 are a strong genetic risk factor for development of schizophrenia and cognitive dysfunction. We employed shotgun liquid chromatography-mass spectrometry (LC-MS) proteomic and metabonomic profiling approaches on prefrontal cortex (PFC) and hippocampal (HPC) tissue from Df(16)A+/- mice, a model of the 22q11.2 deletion syndrome. Proteomic results were compared with previous transcriptomic profiling studies of the same brain regions. The aim was to investigate how the combined effect of the 22q11.2 deletion and the corresponding miRNA dysregulation affects the cell biology at the systems level. The proteomic brain profiling analysis revealed PFC and HPC changes in various molecular pathways associated with chromatin remodelling and RNA transcription, indicative of an epigenetic component of the 22q11.2DS. Further, alterations in glycolysis/gluconeogenesis, mitochondrial function and lipid biosynthesis were identified. Metabonomic profiling substantiated the proteomic findings by identifying changes in 22q11.2 deletion syndrome (22q11.2DS)-related pathways, such as changes in ceramide phosphoethanolamines, sphingomyelin, carnitines, tyrosine derivates and panthothenic acid. The proteomic findings were confirmed using selected reaction monitoring mass spectrometry, validating decreased levels of several proteins encoded on 22q11.2, increased levels of the computationally predicted putative miR-185 targets UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT1) and kinesin heavy chain isoform 5A and alterations in the non-miR-185 targets serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform, neurofilament light chain and vesicular glutamate transporter 1. Furthermore, alterations in the proteins associated with mammalian target of rapamycin signalling were detected in the PFC and with glutamatergic signalling in the hippocampus. Based on the proteomic and metabonomic findings, we were able to develop a schematic model summarizing the most prominent molecular network findings in the Df(16)A+/- mouse. Interestingly, the implicated pathways can be linked to one of the most consistent and strongest proteomic candidates, (OGT1), which is a predicted miR-185 target. Our results provide novel insights into system-biological mechanisms associated with the 22q11DS, which may be linked to cognitive dysfunction and an increased risk to develop schizophrenia. Further investigation of these pathways could help to identify novel drug targets for the treatment of schizophrenia.
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27
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Gagnon J, Daou S, Zamorano N, Iannantuono NVG, Hammond-Martel I, Mashtalir N, Bonneil E, Wurtele H, Thibault P, Affar EB. Undetectable histone O-GlcNAcylation in mammalian cells. Epigenetics 2016; 10:677-91. [PMID: 26075789 DOI: 10.1080/15592294.2015.1060387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
O-GlcNAcylation is a posttranslational modification catalyzed by the O-Linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) and reversed by O-GlcNAcase (OGA). Numerous transcriptional regulators, including chromatin modifying enzymes, transcription factors, and co-factors, are targeted by O-GlcNAcylation, indicating that this modification is central for chromatin-associated processes. Recently, OGT-mediated O-GlcNAcylation was reported to be a novel histone modification, suggesting a potential role in directly coordinating chromatin structure and function. In contrast, using multiple biochemical approaches, we report here that histone O-GlcNAcylation is undetectable in mammalian cells. Conversely, O-GlcNAcylation of the transcription regulators Host Cell Factor-1 (HCF-1) and Ten-Eleven Translocation protein 2 (TET2) could be readily observed. Our study raises questions on the occurrence and abundance of O-GlcNAcylation as a histone modification in mammalian cells and reveals technical complications regarding the detection of genuine protein O-GlcNAcylation. Therefore, the identification of the specific contexts in which histone O-GlcNAcylation might occur is still to be established.
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Key Words
- Chromatin
- Epigenetics
- H2B K120ub, Histone H2B lysine 120 monoubiquitination
- H2B S112 O-GlcNAc, Histone H2B serine 112 O-GlcNAc
- HCF-1
- HCF-1, Host Cell Factor-1
- Histone
- O-GlcNAc
- O-GlcNAc, O-Linked N-acetylglucosamine
- O-GlcNAcylation
- OGA, O-GlcNAcase
- OGT
- OGT, O-Linked N-acetylglucosamine transferase
- PUGNAc, O-(2-acetamido-2-deoxyglucopyranosylidene) amino N-phenylcarbamate
- Polycomb
- TET2
- TET2, Ten-Eleven Translocation protein 2
- UDP-GlcNAc, Uridine Diphosphate N-Acetylglucosamine
- WGA, Wheat Germ Agglutinin.
- posttranslational modification
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Affiliation(s)
- Jessica Gagnon
- a Maisonneuve-Rosemont Hospital Research Center and Department of Medicine; University of Montréal ; Montréal, Québec , Canada
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28
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Shi J, Sharif S, Ruijtenbeek R, Pieters RJ. Activity Based High-Throughput Screening for Novel O-GlcNAc Transferase Substrates Using a Dynamic Peptide Microarray. PLoS One 2016; 11:e0151085. [PMID: 26960196 PMCID: PMC4784888 DOI: 10.1371/journal.pone.0151085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
O-GlcNAcylation is a reversible and dynamic protein post-translational modification in mammalian cells. The O-GlcNAc cycle is catalyzed by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). O-GlcNAcylation plays important role in many vital cellular events including transcription, cell cycle regulation, stress response and protein degradation, and altered O-GlcNAcylation has long been implicated in cancer, diabetes and neurodegenerative diseases. Recently, numerous approaches have been developed to identify OGT substrates and study their function, but there is still a strong demand for highly efficient techniques. Here we demonstrated the utility of the peptide microarray approach to discover novel OGT substrates and study its specificity. Interestingly, the protein RBL-2, which is a key regulator of entry into cell division and may function as a tumor suppressor, was identified as a substrate for three isoforms of OGT. Using peptide Ala scanning, we found Ser 420 is one possible O-GlcNAc site in RBL-2. Moreover, substitution of Ser 420, on its own, inhibited OGT activity, raising the possibility of mechanism-based development for selective OGT inhibitors. This approach will prove useful for both discovery of novel OGT substrates and studying OGT specificity.
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Affiliation(s)
- Jie Shi
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Suhela Sharif
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- PamGene International BV, ‘s-Hertogenbosch, The Netherlands
| | - Roland J. Pieters
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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29
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Rahaman SNA, Mat Yusop J, Mohamed-Hussein ZA, Ho KL, Teh AH, Waterman J, Ng CL. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein. Acta Crystallogr F Struct Biol Commun 2016; 72:207-13. [PMID: 26919524 PMCID: PMC4774879 DOI: 10.1107/s2053230x16002016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/02/2016] [Indexed: 01/17/2023] Open
Abstract
C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parameters a = 59.32, b = 65.35, c = 95.05 Å. The calculated Matthews coefficient (VM) value of 2.27 Å(3) Da(-1) suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%.
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Affiliation(s)
| | - Jastina Mat Yusop
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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30
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Janetzko J, Walker S. The making of a sweet modification: structure and function of O-GlcNAc transferase. J Biol Chem 2014; 289:34424-32. [PMID: 25336649 DOI: 10.1074/jbc.r114.604405] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
O-GlcNAc transferase is an essential mammalian enzyme responsible for transferring a single GlcNAc moiety from UDP-GlcNAc to specific serine/threonine residues of hundreds of nuclear and cytoplasmic proteins. This modification is dynamic and has been implicated in numerous signaling pathways. An unexpected second function for O-GlcNAc transferase as a protease involved in cleaving the epigenetic regulator HCF-1 has also been reported. Recent structural and biochemical studies that provide insight into the mechanism of glycosylation and HCF-1 cleavage will be described, with outstanding questions highlighted.
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Affiliation(s)
- John Janetzko
- the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Suzanne Walker
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115 and
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