1
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [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: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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2
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Yu H, Liu D, Zhang Y, Tang R, Fan X, Mao S, Lv L, Chen F, Qin H, Zhang Z, van Aalten DMF, Yang B, Yuan K. Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning. eLife 2024; 13:e91269. [PMID: 38619103 PMCID: PMC11018347 DOI: 10.7554/elife.91269] [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: 07/23/2023] [Accepted: 03/14/2024] [Indexed: 04/16/2024] Open
Abstract
O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, we developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the O-GlcNAc interactome in major brain regions of Drosophila and found that components of the translational machinery, particularly ribosomal subunits, were abundantly O-GlcNAcylated in the mushroom body of Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. Our study provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila, and suggests a possibility that O-GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain.
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Affiliation(s)
- Haibin Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Dandan Liu
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Yaowen Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Xunan Fan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
| | - Hongtao Qin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan UniversityChangshaChina
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
| | - Daan MF van Aalten
- Department of Molecular Biology and Genetics, University of AarhusAarhusDenmark
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, HangzhouZhejiangChina
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaChina
- The Biobank of Xiangya Hospital, Central South UniversityChangshaChina
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3
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Vang S, Helton ES, Guo Y, Burpee B, Rose E, Easter M, Bollenbecker S, Hirsch MJ, Matthews EL, Jones LI, Howze PH, Rajasekaran V, Denson R, Cochran P, Attah IK, Olson H, Clair G, Melkani G, Krick S, Barnes JW. O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis. Front Immunol 2024; 15:1387197. [PMID: 38665916 PMCID: PMC11043510 DOI: 10.3389/fimmu.2024.1387197] [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: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic pulmonary disease that is characterized by an excessive accumulation of extracellular matrix (ECM) proteins (e.g. collagens) in the parenchyma, which ultimately leads to respiratory failure and death. While current therapies exist to slow the progression, no therapies are available to resolve fibrosis. Methods We characterized the O-linked N-Acetylglucosamine (O-GlcNAc) transferase (OGT)/O-GlcNAc axis in IPF using single-cell RNA-sequencing (scRNA-seq) data and human lung sections and isolated fibroblasts from IPF and non-IPF donors. The underlying mechanism(s) of IPF were further investigated using multiple experimental models to modulate collagen expression and accumulation by genetically and pharmacologically targeting OGT. Furthermore, we hone in on the transforming growth factor-beta (TGF-β) effector molecule, Smad3, by co-expressing it with OGT to determine if it is modified and its subsequent effect on Smad3 activation. Results We found that OGT and O-GlcNAc levels are upregulated in patients with IPF compared to non-IPF. We report that the OGT regulates collagen deposition and fibrosis resolution, which is an evolutionarily conserved process demonstrated across multiple species. Co-expression of OGT and Smad3 showed that Smad3 is O-GlcNAc modified. Blocking OGT activity resulted in decreased phosphorylation at Ser-423/425 of Smad3 attenuating the effects of TGF-β1 induced collagen expression/deposition. Conclusion OGT inhibition or knockdown successfully blocked and reversed collagen expression and accumulation, respectively. Smad3 is discovered to be a substrate of OGT and its O-GlcNAc modification(s) directly affects its phosphorylation state. These data identify OGT as a potential target in pulmonary fibrosis resolution, as well as other diseases that might have aberrant ECM/collagen accumulation.
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Affiliation(s)
- Shia Vang
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Eric Scott Helton
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yiming Guo
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bailey Burpee
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Elex Rose
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Molly Easter
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Seth Bollenbecker
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Meghan June Hirsch
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Emma Lea Matthews
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Luke Isaac Jones
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Patrick Henry Howze
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vasanthi Rajasekaran
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Rebecca Denson
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Phillip Cochran
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Isaac Kwame Attah
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Heather Olson
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Girish Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stefanie Krick
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jarrod Wesley Barnes
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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Hu YJ, Zhang X, Lv HM, Liu Y, Li SZ. Protein O-GlcNAcylation: The sweet hub in liver metabolic flexibility from a (patho)physiological perspective. Liver Int 2024; 44:293-315. [PMID: 38110988 DOI: 10.1111/liv.15812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/20/2023]
Abstract
O-GlcNAcylation is a dynamic, reversible and atypical O-glycosylation that regulates various cellular physiological processes via conformation, stabilisation, localisation, chaperone interaction or activity of target proteins. The O-GlcNAcylation cycle is precisely controlled by collaboration between O-GlcNAc transferase and O-GlcNAcase. Uridine-diphosphate-N-acetylglucosamine, the sole donor of O-GlcNAcylation produced by the hexosamine biosynthesis pathway, is controlled by the input of glucose, glutamine, acetyl coenzyme A and uridine triphosphate, making it a sensor of the fluctuation of molecules, making O-GlcNAcylation a pivotal nutrient sensor for the metabolism of carbohydrates, amino acids, lipids and nucleotides. O-GlcNAcylation, particularly prevalent in liver, is the core hub for controlling systemic glucose homeostasis due to its nutritional sensitivity and precise spatiotemporal regulation of insulin signal transduction. The pathology of various liver diseases has highlighted hepatic metabolic disorder and dysfunction, and abnormal O-GlcNAcylation also plays a specific pathological role in these processes. Therefore, this review describes the unique features of O-GlcNAcylation and its dynamic homeostasis maintenance. Additionally, it explains the underlying nutritional sensitivity of O-GlcNAcylation and discusses its mechanism of spatiotemporal modulation of insulin signal transduction and liver metabolic homeostasis during the fasting and feeding cycle. This review emphasises the pathophysiological implications of O-GlcNAcylation in nonalcoholic fatty liver disease, nonalcoholic steatohepatitis and hepatic fibrosis, and focuses on the adverse effects of hyper O-GlcNAcylation on liver cancer progression and metabolic reprogramming.
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Affiliation(s)
- Ya-Jie Hu
- Key Laboratory of Bovine Disease Control in Northeast China of Ministry of Agriculture and Rural affairs of the People's Republic of China, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xu Zhang
- Key Laboratory of Bovine Disease Control in Northeast China of Ministry of Agriculture and Rural affairs of the People's Republic of China, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hong-Ming Lv
- Key Laboratory of Bovine Disease Control in Northeast China of Ministry of Agriculture and Rural affairs of the People's Republic of China, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yang Liu
- Key Laboratory of Bovine Disease Control in Northeast China of Ministry of Agriculture and Rural affairs of the People's Republic of China, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shi-Ze Li
- Key Laboratory of Bovine Disease Control in Northeast China of Ministry of Agriculture and Rural affairs of the People's Republic of China, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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5
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Weerawarna PM, Schiefer IT, Soares P, Fox S, Morimoto RI, Melani RD, Kelleher NL, Luan CH, Silverman RB. Target Identification of a Class of Pyrazolone Protein Aggregation Inhibitor Therapeutics for Amyotrophic Lateral Sclerosis. ACS CENTRAL SCIENCE 2024; 10:87-103. [PMID: 38292603 PMCID: PMC10823514 DOI: 10.1021/acscentsci.3c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure, and current treatment options are very limited. Previously, we performed a high-throughput screen to identify small molecules that inhibit protein aggregation caused by a mutation in the gene that encodes superoxide dismutase 1 (SOD1), which is responsible for about 25% of familial ALS. This resulted in three hit series of compounds that were optimized over several years to give three compounds that were highly active in a mutant SOD1 ALS model. Here we identify the target of two of the active compounds (6 and 7) with the use of photoaffinity labeling, chemical biology reporters, affinity purification, proteomic analysis, and fluorescent/cellular thermal shift assays. Evidence is provided to demonstrate that these two pyrazolone compounds directly interact with 14-3-3-E and 14-3-3-Q isoforms, which have chaperone activity and are known to interact with mutant SOD1G93A aggregates and become insoluble in the subcellular JUNQ compartment, leading to apoptosis. Because protein aggregation is the hallmark of all neurodegenerative diseases, knowledge of the target compounds that inhibit protein aggregation allows for the design of more effective molecules for the treatment of ALS and possibly other neurodegenerative diseases.
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Affiliation(s)
- Pathum M. Weerawarna
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Isaac T. Schiefer
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Pedro Soares
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Susan Fox
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard I. Morimoto
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department
of Chemistry and Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics
Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Chi-Hao Luan
- High
Throughput
Analysis Laboratory, Chemistry of Life Processes Institute, and Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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6
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Kim DY, Park J, Han IO. Hexosamine biosynthetic pathway and O-GlcNAc cycling of glucose metabolism in brain function and disease. Am J Physiol Cell Physiol 2023; 325:C981-C998. [PMID: 37602414 DOI: 10.1152/ajpcell.00191.2023] [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: 05/23/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023]
Abstract
Impaired brain glucose metabolism is considered a hallmark of brain dysfunction and neurodegeneration. Disruption of the hexosamine biosynthetic pathway (HBP) and subsequent O-linked N-acetylglucosamine (O-GlcNAc) cycling has been identified as an emerging link between altered glucose metabolism and defects in the brain. Myriads of cytosolic and nuclear proteins in the nervous system are modified at serine or threonine residues with a single N-acetylglucosamine (O-GlcNAc) molecule by O-GlcNAc transferase (OGT), which can be removed by β-N-acetylglucosaminidase (O-GlcNAcase, OGA). Homeostatic regulation of O-GlcNAc cycling is important for the maintenance of normal brain activity. Although significant evidence linking dysregulated HBP metabolism and aberrant O-GlcNAc cycling to induction or progression of neuronal diseases has been obtained, the issue of whether altered O-GlcNAcylation is causal in brain pathogenesis remains uncertain. Elucidation of the specific functions and regulatory mechanisms of individual O-GlcNAcylated neuronal proteins in both normal and diseased states may facilitate the identification of novel therapeutic targets for various neuronal disorders. The information presented in this review highlights the importance of HBP/O-GlcNAcylation in the neuronal system and summarizes the roles and potential mechanisms of O-GlcNAcylated neuronal proteins in maintaining normal brain function and initiation and progression of neurological diseases.
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Affiliation(s)
- Dong Yeol Kim
- Department of Biomedical Science, Program in Biomedical Science and Engineering, College of Medicine, Inha University, Incheon, South Korea
| | - Jiwon Park
- Department of Biomedical Science, Program in Biomedical Science and Engineering, College of Medicine, Inha University, Incheon, South Korea
| | - Inn-Oc Han
- Department of Biomedical Science, Program in Biomedical Science and Engineering, College of Medicine, Inha University, Incheon, South Korea
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7
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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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8
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Phillips NJ, Vinaithirthan BM, Oses-Prieto JA, Chalkley RJ, Burlingame AL. Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes. Mol Cell Proteomics 2023; 22:100497. [PMID: 36642223 PMCID: PMC9971285 DOI: 10.1016/j.mcpro.2023.100497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/17/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
New protein synthesis is regulated both at the level of mRNA transcription and translation. RNA-Seq is effective at measuring levels of mRNA expression, but techniques to monitor mRNA translation are much more limited. Previously, we reported results from O-propargyl-puromycin (OPP) labeling of proteins undergoing active translation in a 2-h time frame, followed by biotinylation using click chemistry, affinity purification, and on-bead digestion to identify nascent proteins by mass spectrometry (OPP-ID). As with any on-bead digestion protocol, the problem of nonspecific binders complicated the rigorous categorization of nascent proteins by OPP-ID. Here, we incorporate a chemically cleavable linker, Dde biotin-azide, into the protocol (OPP-IDCL) to provide specific release of modified proteins from the streptavidin beads. Following capture, the Dde moiety is readily cleaved with 2% hydrazine, releasing nascent polypeptides bearing OPP plus a residual C3H8N4 tag. When results are compared side by side with the original OPP-ID method, change to a cleavable linker led to a dramatic reduction in the number of background proteins detected in controls and a concomitant increase in the number of proteins that could be characterized as newly synthesized. We evaluated the method's ability to detect nascent proteins at various submilligram protein input levels and showed that, when starting with only 100 μg of protein, ∼1500 nascent proteins could be identified with low background. Upon treatment of K562 cells with MLN128, a potent inhibitor of the mammalian target of rapamycin, prior to OPP treatment, we identified 1915 nascent proteins, the majority of which were downregulated upon inhibitor treatment. Repressed proteins with log2 FC <-1 revealed a complex network of functionally interacting proteins, with the largest cluster associated with translational initiation. Overall, incorporation of the Dde biotin-azide cleavable linker into our protocol has increased the depth and accuracy of profiling of nascent protein networks.
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Affiliation(s)
- Nancy J Phillips
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bala M Vinaithirthan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA.
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9
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Lu Q, Zhang X, Liang T, Bai X. O-GlcNAcylation: an important post-translational modification and a potential therapeutic target for cancer therapy. Mol Med 2022; 28:115. [PMID: 36104770 PMCID: PMC9476278 DOI: 10.1186/s10020-022-00544-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/07/2022] [Indexed: 02/07/2023] Open
Abstract
O-linked β-d-N-acetylglucosamine (O-GlcNAc) is an important post-translational modification of serine or threonine residues on thousands of proteins in the nucleus and cytoplasm of all animals and plants. In eukaryotes, only two conserved enzymes are involved in this process. O-GlcNAc transferase is responsible for adding O-GlcNAc to proteins, while O-GlcNAcase is responsible for removing it. Aberrant O-GlcNAcylation is associated with a variety of human diseases, such as diabetes, cancer, neurodegenerative diseases, and cardiovascular diseases. Numerous studies have confirmed that O-GlcNAcylation is involved in the occurrence and progression of cancers in multiple systems throughout the body. It is also involved in regulating multiple cancer hallmarks, such as metabolic reprogramming, proliferation, invasion, metastasis, and angiogenesis. In this review, we first describe the process of O-GlcNAcylation and the structure and function of O-GlcNAc cycling enzymes. In addition, we detail the occurrence of O-GlcNAc in various cancers and the role it plays. Finally, we discuss the potential of O-GlcNAc as a promising biomarker and novel therapeutic target for cancer diagnosis, treatment, and prognosis.
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10
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Dupas T, Betus C, Blangy-Letheule A, Pelé T, Persello A, Denis M, Lauzier B. An overview of tools to decipher O-GlcNAcylation from historical approaches to new insights. Int J Biochem Cell Biol 2022; 151:106289. [PMID: 36031106 DOI: 10.1016/j.biocel.2022.106289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
O-GlcNAcylation is a post-translational modification which affects approximately 5000 human proteins. Its involvement has been shown in many if not all biological processes. Variations in O-GlcNAcylation levels can be associated with the development of diseases. Deciphering the role of O-GlcNAcylation is an important issue to (i) understand its involvement in pathophysiological development and (ii) develop new therapeutic strategies to modulate O-GlcNAc levels. Over the past 30 years, despite the development of several approaches, knowledge of its role and regulation have remained limited. This review proposes an overview of the currently available tools to study O-GlcNAcylation and identify O-GlcNAcylated proteins. Briefly, we discuss pharmacological modulators, methods to study O-GlcNAcylation levels and approaches for O-GlcNAcylomic profiling. This review aims to contribute to a better understanding of the methods used to study O-GlcNAcylation and to promote efforts in the development of new strategies to explore this promising modification.
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Affiliation(s)
- Thomas Dupas
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France.
| | - Charlotte Betus
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France; Department of Pharmacology and Physiology, University of Montreal, Montreal, QC H3T 1C5, Canada; CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | - Thomas Pelé
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Antoine Persello
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | - Manon Denis
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France; Department of Pharmacology and Physiology, University of Montreal, Montreal, QC H3T 1C5, Canada; CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Benjamin Lauzier
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
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11
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Xu S, Zheng J, Xiao H, Wu R. Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells. Anal Chem 2022; 94:3343-3351. [PMID: 35132862 DOI: 10.1021/acs.analchem.1c05438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycoproteins with diverse glycans are essential to human cells, and subtle differences in glycan structures may result in entirely different functions. One typical example is proteins modified with O-linked β-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc) (the Tn antigen), in which the two glycans have very similar structures and identical chemical compositions, making them extraordinarily challenging to be distinguished. Here, we developed an effective method benefiting from selective enrichment and the enzymatic specificity to simultaneously identify and distinguish glycoproteins with O-GlcNAc and O-GalNAc. Metabolic labeling was combined with bioorthogonal chemistry for enriching glycoproteins modified with O-GlcNAc and O-GalNAc. Then, the enzymatic reaction with galactose oxidase was utilized to specifically oxidize O-GalNAc, but not O-GlcNAc, generating the different tags between glycopeptides with O-GlcNAc and O-GalNAc that can be easily distinguishable by mass spectrometry (MS). Among O-GlcNAcylated proteins commonly identified in three types of human cells, those related to transcription and RNA binding are highly enriched. Cell-specific features are also revealed. Among glycoproteins exclusively in Jurkat cells, those involved in human T-lymphotropic virus type 1 (HTLV-1) infection are overrepresented, which is consistent with the cell line source and suggests that protein O-GlcNAcylation participated in the response to the virus infection. Furthermore, glycoproteins with the Tn antigen have different subcellular distributions in different cells, which may be attributed to the distinct mechanisms for the formation of protein O-GalNAcylation.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jiangnan Zheng
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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12
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Revealing functional significance of interleukin‐2 glycoproteoforms enabled by expressed serine ligation. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100914] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Jacobsen MT, Spaltenstein P, Giesler RJ, Chou DHC, Kay MS. Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools. Methods Mol Biol 2022; 2530:81-107. [PMID: 35761044 DOI: 10.1007/978-1-0716-2489-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Maintaining high, or even sufficient, solubility of every peptide segment in chemical protein synthesis (CPS) remains a critical challenge; insolubility of just a single peptide segment can thwart a total synthesis venture. Multiple approaches have been used to address this challenge, most commonly by employing a chemical tool to temporarily improve peptide solubility. In this chapter, we discuss chemical tools for introducing semipermanent solubilizing sequences (termed helping hands) at the side chains of Lys and Glu residues. We describe the synthesis, incorporation by Fmoc-SPPS, and cleavage conditions for utilizing these two tools. For Lys sites, we discuss the Fmoc-Ddap-OH dimedone-based linker, which is achiral, synthesized in one step, can be introduced directly at primary amines, and is removed using hydroxylamine (or hydrazine). For Glu sites, we detail the new Fmoc-SPPS building block, Fmoc-Glu(AlHx)-OH, which can be prepared in an efficient process over two purifications. Solubilizing sequences are introduced directly on-resin and later cleaved with palladium-catalyzed transfer under aqueous conditions to restore a native Glu side chain. These two chemical tools are straightforward to prepare and implement, and we anticipate continued usage in "difficult" peptide segments following the protocols described herein.
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Affiliation(s)
- Michael T Jacobsen
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Riley J Giesler
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Danny Hung-Chieh Chou
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Michael S Kay
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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14
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Xu Y, Zhang H. Putting the pieces together: mapping the O-glycoproteome. Curr Opin Biotechnol 2021; 71:130-136. [PMID: 34358979 PMCID: PMC8629430 DOI: 10.1016/j.copbio.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/26/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Protein glycosylation is the most diverse and omnipresent protein modification. Glycosylation provides glycoproteins with important structural and functional properties to facilitate critical biological processes. Despite the significance of protein glycosylation, the investigation of glycoproteome, especially O-linked glycoproteome, remains elusive due to the lack of a comprehensive methodology to conform with the diversity of O-linked glycoforms of O-linked glycoproteins. In recent years, mass spectrometry has become an indispensable tool for the characterization of O-linked glycosylated proteins across biological systems. We herein highlight the recent developments in MS-based O-linked glycoproteomic technologies, quantitative data acquisition strategy and bioinformatic tools, with a special focus on mucin-type O-linked glycosylation.
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Affiliation(s)
- Yuanwei Xu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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15
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Saha A, Bello D, Fernández-Tejada A. Advances in chemical probing of protein O-GlcNAc glycosylation: structural role and molecular mechanisms. Chem Soc Rev 2021; 50:10451-10485. [PMID: 34338261 PMCID: PMC8451060 DOI: 10.1039/d0cs01275k] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Indexed: 12/11/2022]
Abstract
The addition of O-linked-β-D-N-acetylglucosamine (O-GlcNAc) onto serine and threonine residues of nuclear and cytoplasmic proteins is an abundant, unique post-translational modification governing important biological processes. O-GlcNAc dysregulation underlies several metabolic disorders leading to human diseases, including cancer, neurodegeneration and diabetes. This review provides an extensive summary of the recent progress in probing O-GlcNAcylation using mainly chemical methods, with a special focus on discussing mechanistic insights and the structural role of O-GlcNAc at the molecular level. We highlight key aspects of the O-GlcNAc enzymes, including development of OGT and OGA small-molecule inhibitors, and describe a variety of chemoenzymatic and chemical biology approaches for the study of O-GlcNAcylation. Special emphasis is placed on the power of chemistry in the form of synthetic glycopeptide and glycoprotein tools for investigating the site-specific functional consequences of the modification. Finally, we discuss in detail the conformational effects of O-GlcNAc glycosylation on protein structure and stability, relevant O-GlcNAc-mediated protein interactions and its molecular recognition features by biological receptors. Future research in this field will provide novel, more effective chemical strategies and probes for the molecular interrogation of O-GlcNAcylation, elucidating new mechanisms and functional roles of O-GlcNAc with potential therapeutic applications in human health.
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Affiliation(s)
- Abhijit Saha
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
| | - Davide Bello
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
| | - Alberto Fernández-Tejada
- Chemical Immunology Lab, Centre for Cooperative Research in Biosciences, CIC-bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Biscay, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain
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16
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Zhu Q, Yi W. Chemistry-Assisted Proteomic Profiling of O-GlcNAcylation. Front Chem 2021; 9:702260. [PMID: 34249870 PMCID: PMC8267408 DOI: 10.3389/fchem.2021.702260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
The modification on proteins with O-linked N-acetyl-β-D-glucosamine (O-GlcNAcylation) is essential for normal cell physiology. Dysregulation of O-GlcNAcylation leads to many human diseases, such as cancer, diabetes and neurodegenerative diseases. Recently, the functional role of O-GlcNAcylation in different physiological states has been elucidated due to the booming detection technologies. Chemical approaches for the enrichment of O-GlcNAcylated proteins combined with mass spectrometry-based proteomics enable the profiling of protein O-GlcNAcylation in a system-wide level. In this review, we summarize recent progresses on the enrichment and proteomic profiling of protein O-GlcNAcylation.
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Affiliation(s)
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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17
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Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
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Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
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18
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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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19
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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20
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Wu D, Jin J, Qiu Z, Liu D, Luo H. Functional Analysis of O-GlcNAcylation in Cancer Metastasis. Front Oncol 2020; 10:585288. [PMID: 33194731 PMCID: PMC7653022 DOI: 10.3389/fonc.2020.585288] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
One common and reversible type of post-translational modification (PTM) is the addition of O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), and its dynamic balance is controlled by O-GlcNAc transferase (OGT) and glycoside hydrolase O-GlcNAcase (OGA) through the addition or removal of O-GlcNAc groups. A large amount of research data confirms that proteins regulated by O-GlcNAcylation play a pivotal role in cells. In particularly, imbalanced levels of OGT and O-GlcNAcylation have been found in various types of cancers. Recently, increasing evidence shows that imbalanced O-GlcNAcylation directly or indirectly impacts the process of cancer metastasis. This review summarizes the current understanding of the influence of O-GlcNAc-proteins on the regulation of cancer metastasis. It will provide a theoretical basis to further elucidate of the molecular mechanisms underlying cancer emergence and progression.
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Affiliation(s)
- Donglu Wu
- School of Clinical Medical, Changchun University of Chinese Medicine, Changchun, China.,Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jingji Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhidong Qiu
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Haoming Luo
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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21
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Chatham JC, Zhang J, Wende AR. Role of O-Linked N-Acetylglucosamine Protein Modification in Cellular (Patho)Physiology. Physiol Rev 2020; 101:427-493. [PMID: 32730113 DOI: 10.1152/physrev.00043.2019] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In the mid-1980s, the identification of serine and threonine residues on nuclear and cytoplasmic proteins modified by a N-acetylglucosamine moiety (O-GlcNAc) via an O-linkage overturned the widely held assumption that glycosylation only occurred in the endoplasmic reticulum, Golgi apparatus, and secretory pathways. In contrast to traditional glycosylation, the O-GlcNAc modification does not lead to complex, branched glycan structures and is rapidly cycled on and off proteins by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), respectively. Since its discovery, O-GlcNAcylation has been shown to contribute to numerous cellular functions, including signaling, protein localization and stability, transcription, chromatin remodeling, mitochondrial function, and cell survival. Dysregulation in O-GlcNAc cycling has been implicated in the progression of a wide range of diseases, such as diabetes, diabetic complications, cancer, cardiovascular, and neurodegenerative diseases. This review will outline our current understanding of the processes involved in regulating O-GlcNAc turnover, the role of O-GlcNAcylation in regulating cellular physiology, and how dysregulation in O-GlcNAc cycling contributes to pathophysiological processes.
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Affiliation(s)
- John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama; and Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - Jianhua Zhang
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama; and Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - Adam R Wende
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama; and Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
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22
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Targeting O-GlcNAcylation to develop novel therapeutics. Mol Aspects Med 2020; 79:100885. [PMID: 32736806 DOI: 10.1016/j.mam.2020.100885] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 04/21/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022]
Abstract
O-linked β-D-N-acetylglucosamine (O-GlcNAc) is an abundant post-translational modification (PTM) that modifies the serine or threonine residues of thousands of proteins in the nucleus, cytoplasm and mitochondria. Being a major "nutrient sensor" in cells, the O-GlcNAc pathway is sensitive to cellular metabolic states. Extensive crosstalk is observed between O-GlcNAcylation and protein phosphorylation. O-GlcNAc regulates protein functions at multiple levels, including enzymatic activity, transcriptional activity, subcellular localization, intermolecular interactions and degradation. Abnormal O-GlcNAcylation is associated with many human diseases including cancer, diabetes and neurodegenerative diseases. Though research on O-GlcNAc is still in its infantry, accumulating evidence suggest O-GlcNAcylation to be a promising therapeutic target. In this review, we briefly discuss the basic features of this PTM, the O-GlcNAc signaling pathway, its regulatory functions on different proteins, and its involvement in human diseases. We hope this review will provide insights to researchers who study human disease, as well as researchers who are interested in the fundamental roles of O-GlcNAcylation in all cells.
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23
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Escobar EE, King DT, Serrano-Negrón JE, Alteen MG, Vocadlo DJ, Brodbelt JS. Precision Mapping of O-Linked N-Acetylglucosamine Sites in Proteins Using Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2020; 142:11569-11577. [PMID: 32510947 DOI: 10.1021/jacs.0c04710] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Despite its central importance as a regulator of cellular physiology, identification and precise mapping of O-linked N-acetylglucosamine (O-GlcNAc) post-translational modification (PTM) sites in proteins by mass spectrometry (MS) remains a considerable technical challenge. This is due in part to cleavage of the glycosidic bond occurring prior to the peptide backbone during collisionally activated dissociation (CAD), which leads to generation of characteristic oxocarbenium ions and impairs glycosite localization. Herein, we leverage CAD-induced oxocarbenium ion generation to trigger ultraviolet photodissociation (UVPD), an alternate high-energy deposition method that offers extensive fragmentation of peptides while leaving the glycosite intact. Upon activation using UV laser pulses, efficient photodissociation of glycopeptides is achieved with production of multiple sequence ions that enable robust and precise localization of O-GlcNAc sites. Application of this method to tryptic peptides originating from O-GlcNAcylated proteins TAB1 and Polyhomeotic confirmed previously reported O-GlcNAc sites in TAB1 (S395 and S396) and uncovered new sites within both proteins. We expect this strategy will complement existing MS/MS methods and be broadly useful for mapping O-GlcNAcylated residues of both proteins and proteomes.
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Affiliation(s)
- Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dustin T King
- Department of Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jesús E Serrano-Negrón
- Department of Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew G Alteen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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24
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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25
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Liu L, Li L, Ma C, Shi Y, Liu C, Xiao Z, Zhang Y, Tian F, Gao Y, Zhang J, Ying W, Wang PG, Zhang L. O-GlcNAcylation of Thr 12/Ser 56 in short-form O-GlcNAc transferase (sOGT) regulates its substrate selectivity. J Biol Chem 2019; 294:16620-16633. [PMID: 31527085 DOI: 10.1074/jbc.ra119.009085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/11/2019] [Indexed: 02/05/2023] Open
Abstract
O-GlcNAcylation is a ubiquitous protein glycosylation playing different roles on variant proteins. O-GlcNAc transferase (OGT) is the unique enzyme responsible for the sugar addition to nucleocytoplasmic proteins. Recently, multiple O-GlcNAc sites have been observed on short-form OGT (sOGT) and nucleocytoplasmic OGT (ncOGT), both of which locate in the nucleus and cytoplasm in cell. Moreover, O-GlcNAcylation of Ser389 in ncOGT (1036 amino acids) affects its nuclear translocation in HeLa cells. To date, the major O-GlcNAcylation sites and their roles in sOGT remain unknown. Here, we performed LC-MS/MS and mutational analyses to seek the major O-GlcNAcylation site on sOGT. We identified six O-GlcNAc sites in the tetratricopeptide repeat domain in sOGT, with Thr12 and Ser56 being two "key" sites. Thr12 is a dominant O-GlcNAcylation site, whereas the modification of Ser56 plays a role in regulating sOGT O-GlcNAcylation, partly through Thr12 In vitro activity and pulldown assays demonstrated that O-GlcNAcylation does not affect sOGT activity but does affect sOGT-interacting proteins. In HEK293T cells, S56A bound to and hence glycosylated more proteins in contrast to T12A and WT sOGT. By proteomic and bioinformatics analyses, we found that T12A and S56A differed in substrate proteins (e.g. HNRNPU and PDCD6IP), which eventually affected cell cycle progression and/or cell proliferation. These findings demonstrate that O-GlcNAcylation modulates sOGT substrate selectivity and affects its role in the cell. The data also highlight the regulatory role of O-GlcNAcylation at Thr12 and Ser56.
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Affiliation(s)
- Li Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Ling Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Cheng Ma
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yangde Shi
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Congcong Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Zikang Xiao
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China.,West China-Washington Mitochondria and Metabolism Research Center, Key Laboratory of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yang Gao
- School of medicine, Nankai University, Tianjin 300071, China
| | - Jie Zhang
- School of medicine, Nankai University, Tianjin 300071, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Peng George Wang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.,Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Lianwen Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
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26
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Zachara NE. Critical observations that shaped our understanding of the function(s) of intracellular glycosylation (O-GlcNAc). FEBS Lett 2018; 592:3950-3975. [PMID: 30414174 DOI: 10.1002/1873-3468.13286] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
Abstract
Almost 100 years after the first descriptions of proteins conjugated to carbohydrates (mucins), several studies suggested that glycoproteins were not restricted to the serum, extracellular matrix, cell surface, or endomembrane system. In the 1980s, key data emerged demonstrating that intracellular proteins were modified by monosaccharides of O-linked β-N-acetylglucosamine (O-GlcNAc). Subsequently, this modification was identified on thousands of proteins that regulate cellular processes as diverse as protein aggregation, localization, post-translational modifications, activity, and interactions. In this Review, we will highlight critical discoveries that shaped our understanding of the molecular events underpinning the impact of O-GlcNAc on protein function, the role that O-GlcNAc plays in maintaining cellular homeostasis, and our understanding of the mechanisms that regulate O-GlcNAc-cycling.
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Affiliation(s)
- Natasha E Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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27
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Thompson JW, Sorum AW, Hsieh-Wilson LC. Deciphering the Functions of O-GlcNAc Glycosylation in the Brain: The Role of Site-Specific Quantitative O-GlcNAcomics. Biochemistry 2018; 57:4010-4018. [PMID: 29936833 PMCID: PMC6058732 DOI: 10.1021/acs.biochem.8b00516] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The dynamic posttranslational modification O-linked β- N-acetylglucosamine glycosylation (O-GlcNAcylation) is present on thousands of intracellular proteins in the brain. Like phosphorylation, O-GlcNAcylation is inducible and plays important functional roles in both physiology and disease. Recent advances in mass spectrometry (MS) and bioconjugation methods are now enabling the mapping of O-GlcNAcylation events to individual sites in proteins. However, our understanding of which glycosylation events are necessary for regulating protein function and controlling specific processes, phenotypes, or diseases remains in its infancy. Given the sheer number of O-GlcNAc sites, methods for identifying promising sites and prioritizing them for time- and resource-intensive functional studies are greatly needed. Revealing sites that are dynamically altered by different stimuli or disease states will likely go a long way in this regard. Here, we describe advanced methods for identifying O-GlcNAc sites on individual proteins and across the proteome and for determining their stoichiometry in vivo. We also highlight emerging technologies for quantitative, site-specific MS-based O-GlcNAc proteomics (O-GlcNAcomics), which allow proteome-wide tracking of O-GlcNAcylation dynamics at individual sites. These cutting-edge technologies are beginning to bridge the gap between the high-throughput cataloguing of O-GlcNAcylated proteins and the relatively low-throughput study of individual proteins. By uncovering the O-GlcNAcylation events that change in specific physiological and disease contexts, these new approaches are providing key insights into the regulatory functions of O-GlcNAc in the brain, including their roles in neuroprotection, neuronal signaling, learning and memory, and neurodegenerative diseases.
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Affiliation(s)
- John W. Thompson
- Department of Chemistry and Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Alexander W. Sorum
- Department of Chemistry and Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Linda C. Hsieh-Wilson
- Department of Chemistry and Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
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28
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Darabedian N, Gao J, Chuh KN, Woo CM, Pratt MR. The Metabolic Chemical Reporter 6-Azido-6-deoxy-glucose Further Reveals the Substrate Promiscuity of O-GlcNAc Transferase and Catalyzes the Discovery of Intracellular Protein Modification by O-Glucose. J Am Chem Soc 2018; 140:7092-7100. [PMID: 29771506 PMCID: PMC6540071 DOI: 10.1021/jacs.7b13488] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic chemical reporters of glycosylation in combination with bioorthogonal reactions have been known for two decades and have been used by many different research laboratories for the identification and visualization of glycoconjugates. More recently, however, they have begun to see utility for the investigation of cellular metabolism and the tolerance of biosynthetic enzymes and glycosyltransferases to different sugars. Here, we take this concept one step further by using the metabolic chemical reporter 6-azido-6-deoxy-glucose (6AzGlc). We show that treatment of mammalian cells with the per- O-acetylated version of 6AzGlc results in robust labeling of a variety of proteins. Notably, the pattern of this labeling was consistent with O-GlcNAc modifications, suggesting that the enzyme O-GlcNAc transferase is quite promiscuous for its donor sugar substrates. To confirm this possibility, we show that 6AzGlc-treatment results in the labeling of known O-GlcNAcylated proteins, that the UDP-6AzGlc donor sugar is indeed produced in living cells, and that recombinant OGT will accept UDP-6AzGlc as a substrate in vitro. Finally, we use proteomics to first identify several bona fide 6AzGlc-modifications in mammalian cells and then an endogenous O-glucose modification on host cell factor. These results support the conclusion that OGT can endogenously modify proteins with both N-acetyl-glucosamine and glucose, raising the possibility that intracellular O-glucose modification may be a widespread modification under certain conditions or in particular tissues.
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Affiliation(s)
- Narek Darabedian
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Jinxu Gao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Kelly N. Chuh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
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29
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Ferron M, Denis M, Persello A, Rathagirishnan R, Lauzier B. Protein O-GlcNAcylation in Cardiac Pathologies: Past, Present, Future. Front Endocrinol (Lausanne) 2018; 9:819. [PMID: 30697194 PMCID: PMC6340935 DOI: 10.3389/fendo.2018.00819] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/31/2018] [Indexed: 01/22/2023] Open
Abstract
O-GlcNAcylation is a ubiquitous and reversible post-translational protein modification that has recently gained renewed interest due to the rapid development of analytical tools and new molecules designed to specifically increase the level of protein O-GlcNAcylation. The level of O-GlcNAc modification appears to have either deleterious or beneficial effects, depending on the context (exposure time, pathophysiological context). While high O-GlcNAcylation levels are mostly reported in chronic diseases, the increase in O-GlcNAc level in acute stresses such as during ischemia reperfusion or hemorrhagic shock is reported to be beneficial in vitro, ex vivo, or in vivo. In this context, an increase in O-GlcNAc levels could be a potential new cardioprotective therapy, but the ambivalent effects of protein O-GlcNAcylation augmentation remains as a key problem to be solved prior to their transfer to the clinic. The emergence of new analytical tools has opened new avenues to decipher the mechanisms underlying the beneficial effects associated with an O-GlcNAc level increase. A better understanding of the exact roles of O-GlcNAc on protein function, targeting or stability will help to develop more targeted approaches. The aim of this review is to discuss the mechanisms and potential beneficial impact of O-GlcNAc modulation, and its potential as a new clinical target in cardiology.
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Affiliation(s)
- Marine Ferron
- Montreal Heart Institute, Montreal, QC, Canada
- l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
- *Correspondence: Marine Ferron
| | - Manon Denis
- l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
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30
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Measuring O-GlcNAc cleavage by OGA and cell lysates on a peptide microarray. Anal Biochem 2017; 532:12-18. [DOI: 10.1016/j.ab.2017.05.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/12/2017] [Accepted: 05/26/2017] [Indexed: 01/27/2023]
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31
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Thompson JW, Griffin ME, Hsieh-Wilson LC. Methods for the Detection, Study, and Dynamic Profiling of O-GlcNAc Glycosylation. Methods Enzymol 2017; 598:101-135. [PMID: 29306432 PMCID: PMC5886303 DOI: 10.1016/bs.mie.2017.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to serine/threonine residues of proteins is a ubiquitous posttranslational modification found in all multicellular organisms. Like phosphorylation, O-GlcNAc glycosylation (O-GlcNAcylation) is inducible and regulates a myriad of physiological and pathological processes. However, understanding the diverse functions of O-GlcNAcylation is often challenging due to the difficulty of detecting and quantifying the modification. Thus, robust methods to study O-GlcNAcylation are essential to elucidate its key roles in the regulation of individual proteins, complex cellular processes, and disease. In this chapter, we describe a set of chemoenzymatic labeling methods to (1) detect O-GlcNAcylation on proteins of interest, (2) monitor changes in both the total levels of O-GlcNAcylation and its stoichiometry on proteins of interest, and (3) enable mapping of O-GlcNAc to specific serine/threonine residues within proteins to facilitate functional studies. First, we outline a procedure for the expression and purification of a multiuse mutant galactosyltransferase enzyme (Y289L GalT). We then describe the use of Y289L GalT to modify O-GlcNAc residues with a functional handle, N-azidoacetylgalactosamine (GalNAz). Finally, we discuss several applications of the copper-catalyzed azide-alkyne cycloaddition "click" reaction to attach various alkyne-containing chemical probes to GalNAz and demonstrate how this functionalization of O-GlcNAc-modified proteins can be used to realize (1)-(3) above. Overall, these methods, which utilize commercially available reagents and standard protein analytical tools, will serve to advance our understanding of the diverse and important functions of O-GlcNAcylation.
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Affiliation(s)
- John W Thompson
- California Institute of Technology, Pasadena, CA, United States
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32
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017. [PMID: 28585084 DOI: 10.1007/s00216-017-04067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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33
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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34
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Selvan N, Williamson R, Mariappa D, Campbell DG, Gourlay R, Ferenbach AT, Aristotelous T, Hopkins-Navratilova I, Trost M, van Aalten DMF. A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nat Chem Biol 2017; 13:882-887. [PMID: 28604694 DOI: 10.1038/nchembio.2404] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 03/14/2017] [Indexed: 01/09/2023]
Abstract
Protein O-GlcNAcylation is a reversible post-translational modification of serines and threonines on nucleocytoplasmic proteins. It is cycled by the enzymes O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (O-GlcNAcase or OGA). Genetic approaches in model organisms have revealed that protein O-GlcNAcylation is essential for early embryogenesis. The Drosophila melanogaster gene supersex combs (sxc), which encodes OGT, is a polycomb gene, whose null mutants display homeotic transformations and die at the pharate adult stage. However, the identities of the O-GlcNAcylated proteins involved and the underlying mechanisms linking these phenotypes to embryonic development are poorly understood. Identification of O-GlcNAcylated proteins from biological samples is hampered by the low stoichiometry of this modification and by limited enrichment tools. Using a catalytically inactive bacterial O-GlcNAcase mutant as a substrate trap, we have enriched the O-GlcNAc proteome of the developing Drosophila embryo, identifying, among others, known regulators of Hox genes as candidate conveyors of OGT function during embryonic development.
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Affiliation(s)
- Nithya Selvan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Ritchie Williamson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - David G Campbell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Robert Gourlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Tonia Aristotelous
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Iva Hopkins-Navratilova
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Division of Gene Regulation and Expression, University of Dundee, Dundee, UK
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35
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Xiao H, Wu R. Global and Site-Specific Analysis Revealing Unexpected and Extensive Protein S-GlcNAcylation in Human Cells. Anal Chem 2017; 89:3656-3663. [PMID: 28234450 DOI: 10.1021/acs.analchem.6b05064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein glycosylation is highly diverse and essential for mammalian cell survival. Heterogeneous glycans may be bound to different amino acid residues, forming multiple types of protein glycosylation. In this work, unexpected protein S-GlcNAcylation on cysteine residues was observed to extensively exist in human cells through global and site-specific analysis of protein GlcNAcylation by mass spectrometry. Three independent experiments produced similar results of many cysteine residues bound to N-acetylglucosamine (GlcNAc). Among well-localized S-GlcNAcylation sites, several motifs with an acidic amino acid around the sites were identified, which strongly suggests that a particular type of enzyme is responsible for this modification. Clustering results show that glycoproteins modified with S-GlcNAc are mainly involved in cell-cell adhesion and gene expression. For the first time, we found that proteins were extensively bound to GlcNAc through the side chains of cysteine residues in human cells, and the current discovery further advances our understanding of protein glycosylation.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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36
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Abstract
O-GlcNAcylation is the modification of serine and threonine residues with β-N-acetylglucosamine (O-GlcNAc) on intracellular proteins. This dynamic modification is attached by O-GlcNAc transferase (OGT) and removed by O-GlcNAcase (OGA) and is a critical regulator of various cellular processes. Furthermore, O-GlcNAcylation is dysregulated in many diseases, such as diabetes, cancer, and Alzheimer's disease. However, the precise role of this modification and its cycling enzymes (OGT and OGA) in normal and disease states remains elusive. This is partially due to the difficulty in studying O-GlcNAcylation with traditional genetic and biochemical techniques. In this review, we will summarize recent progress in chemical approaches to overcome these obstacles. We will cover new inhibitors of OGT and OGA, advances in metabolic labeling and cellular imaging, synthetic approaches to access homogeneous O-GlcNAcylated proteins, and cross-linking methods to identify O-GlcNAc-protein interactions. We will also discuss remaining gaps in our toolbox for studying O-GlcNAcylation and questions of high interest that are yet to be answered.
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Affiliation(s)
- Matthew Worth
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Hao Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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37
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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38
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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