1
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 PMCID: PMC10930906 DOI: 10.3390/cells13050394] [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: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA;
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2
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Long Y, Li Z, Wang L, Ao X, Zhang Z, Chen Q, Zhu D, Liu X, Liu R, Chen B, Zhu H, Su Y. Highly efficient identification of nucleocytoplasmic O-glycosylation by the TurboID-based proximity labeling method in living cells. Biotechnol J 2024; 19:e2300090. [PMID: 37897200 DOI: 10.1002/biot.202300090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Glycosylation is a ubiquitous posttranslational modification and plays an important role in many processes, such as protein stability, folding, processing, and trafficking. Among glycosylation types, O-glycosylation is difficult to analyze due to the complex glycan composition, low abundance and lack of glycosidases to remove the O-glycans. Many methods have been applied to analyze the O-glycosylation of membrane glycoproteins and secreted glycoproteins since the synthesis of O-glycosylation occurred in the Golgi apparatus. In recent years, some O-glycosylation has been reported in the nucleus. In this work, we present a proximity labeling strategy based on TurboID by combining core 1 β1-3 galactosyltransferase (C1GalT1), which has been reported in the nucleus, to characterize nucleocytoplasmic O-glycosylation in living HeLa cells. The O-glycosylated protein C1GalT1 was biotinylated by the proximity labeling method in living HeLa cells overexpressing C1GalT1 fused by TurboID and enriched by streptavidin-coated beads. Following digestion with trypsin and mass spectrometry analysis, 68 high-confidence and 298 putative O-glycosylated sites were identified on 366 peptides mapped to 267 proteins. These results indicated that the proximity labeling method is a highly efficient technique to identify O-glycosylation. Furthermore, the finding of abundant O-glycosylation from nucleocytoplasmic proteins indicates a new pathway of O-glycosylation synthesis in cells.
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Affiliation(s)
- Yunfeng Long
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Zhunjie Li
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, P. R. China
| | - Long Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Xin Ao
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Zhengrong Zhang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Qingjie Chen
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Dan Zhu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
| | - Xinghui Liu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Ruolan Liu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - Banghang Chen
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
| | - He Zhu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Yanting Su
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan, Hubei, P. R. China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, P. R. China
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3
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Rabus JM, Guan S, Schultz LM, Abutokaikah MT, Maître P, Bythell BJ. Protonated α- N-Acetyl Galactose Glycopeptide Dissociation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1745-1752. [PMID: 36018613 DOI: 10.1021/jasms.2c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We recently provided mass spectrometric, H/D labeling, and computational evidence of pyranose to furanose N-acetylated ion isomerization reactions that occurred prior to glycosidic bond cleavage in both O- and N-linked glycosylated amino acid model systems (Guan et al. Phys. Chem. Chem. Phys., 2021, 23, 23256-23266). These reactions occurred irrespective of the glycosidic linkage stereochemistry (α or β) and the N-acetylated hexose structure (GlcNAc or GalNAc). In the present article, we test the generality of the preceding findings by examining threonyl α-GalNAc-glycosylated peptides. We utilize computational chemistry to compare the various dissociation and isomerization pathways accessible with collisional activation. We then interrogate the structure(s) of the resulting charged glycan and peptide fragments with infrared "action" spectroscopy. Isomerization of the original pyranose, the protonated glycopeptide [AT(GalNAc)A+H]+, is predicted to be facile compared to direct dissociation, as is the glycosidic bond cleavage of the newly formed furanose form, i.e., furanose oxazolinium ion structures are predicted to predominate. IR action spectra for the m/z 204, C8H14N1O5+, glycan fragment population support this prediction. The IR action spectra of the complementary m/z 262 peptide fragment were assigned as a mixture of the lowest-energy structures of [ATA+H]+ consistent with the literature. If general, the change to a furanose m/z 204 product ion structure fundamentally alters the ion population available for MS3 dissociation and glycopeptide sequence identification.
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Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Lauren M Schultz
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Institut de Chimie Physique, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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4
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Tang W, Liu D, Nie SP. Food glycomics in food science: recent advances and future perspectives. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Goumenou A, Delaunay N, Pichon V. Recent Advances in Lectin-Based Affinity Sorbents for Protein Glycosylation Studies. Front Mol Biosci 2021; 8:746822. [PMID: 34778373 PMCID: PMC8585745 DOI: 10.3389/fmolb.2021.746822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Glycosylation is one of the most significant post-translational modifications occurring to proteins, since it affects some of their basic properties, such as their half-life or biological activity. The developments in analytical methodologies has greatly contributed to a more comprehensive understanding of the quantitative and qualitative characteristics of the glycosylation state of proteins. Despite those advances, the difficulty of a full characterization of glycosylation still remains, mainly due to the complexity of the glycoprotein and/or glycopeptide mixture especially when they are present in complex biological samples. For this reason, various techniques that allow a prior selective enrichment of exclusively glycosylated proteins or glycopeptides have been developed in the past and are coupled either on- or off- line with separation and detection methods. One of the most commonly implemented enrichment methods includes the use of lectin proteins immobilized on various solid supports. Lectins are a group of different, naturally occurring proteins that share a common characteristic, which concerns their affinity for specific sugar moieties of glycoproteins. This review presents the different formats and conditions for the use of lectins in affinity chromatography and in solid phase extraction, including their use in dispersive mode, along with the recent progress made on either commercial or home-made lectin-based affinity sorbents, which can lead to a fast and automated glycosylation analysis.
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Affiliation(s)
- Anastasia Goumenou
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Nathalie Delaunay
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France.,Sorbonne University, Paris, France
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6
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Kumari M, Tetala KKR. A review on recent advances in the enrichment of glycopeptides and glycoproteins by liquid chromatographic methods: 2016-Present. Electrophoresis 2021; 43:388-402. [PMID: 34757643 DOI: 10.1002/elps.202100172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 01/06/2023]
Abstract
Among various protein post-translational modifications (PTMs), glycosylation has received special attention due to its immense role in molecular interactions, cellular signal transduction, immune response, etc. Aberration in glycan moieties of a glycoprotein is associated with cancer, diabetes, and bacterial and viral infections. In biofluids (plasma, saliva, urine, milk, etc.), glycoproteins are low in abundance and are masked by the presence of high abundant proteins. Hence, prior to their identification using mass spectrometry methods, liquid chromatography (LC)-based approaches were widely used. A general enrichment strategy involves a protein digestion step, followed by LC-based enrichment and desorption of glycopeptides, and enzymatic excision of the glycans. The focus of this review article is to highlight the articles published since 2016 that dealt with different LC-based approaches for glycopeptide and glycoprotein enrichment. The preparation of stationary phases, their surface activation, and ligand immobilization strategies have been discussed in detail. Finally, the major developments and future trends in the field have been summarized.
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Affiliation(s)
- Mona Kumari
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu, India
| | - Kishore K R Tetala
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu, India
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7
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Guan S, Bythell BJ. Evidence of gas-phase pyranose-to-furanose isomerization in protonated peptidoglycans. Phys Chem Chem Phys 2021; 23:23256-23266. [PMID: 34632474 DOI: 10.1039/d1cp03842g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptidoglycans are diverse co- and post-translational modifications of key importance in myriad biological processes. Mass spectrometry is employed to infer their biomolecular sequences and stereochemisties, but little is known about the critical gas-phase dissociation processes involved. Here, using tandem mass spectrometry (MS/MS and MSn), isotopic labelling and high-level simulations, we identify and characterize a facile isomerization reaction that produces furanose N-acetylated ions. This reaction occurs for both O- and N-linked peptidoglycans irrespective of glycosidic linkage stereochemistry (α/β). Dissociation of the glycosidic and other bonds thus occur from the furanose isomer critically altering the reaction feasibility and product ion structures.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 The Chemistry Building, Athens, OH 45701, USA.,Department of Chemistry and Biochemistry, University of Missouri, 1 University Blvd, St. Louis, MO 63121, USA.
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 The Chemistry Building, Athens, OH 45701, USA.,Department of Chemistry and Biochemistry, University of Missouri, 1 University Blvd, St. Louis, MO 63121, USA.
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8
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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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9
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Cui Y, Dong X, Zhang X, Chen C, Fu D, Li X, Liang X. Deciphering the O-Glycosylation of HKU1 Spike Protein With the Dual-Functional Hydrophilic Interaction Chromatography Materials. Front Chem 2021; 9:707235. [PMID: 34485242 PMCID: PMC8414140 DOI: 10.3389/fchem.2021.707235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/13/2021] [Indexed: 01/21/2023] Open
Abstract
HKU1 is a human beta coronavirus and infects host cells via highly glycosylated spike protein (S). The N-glycosylation of HKU1 S has been reported. However, little is known about its O-glycosylation, which hinders the in-depth understanding of its biological functions. Herein, a comprehensive study of O-glycosylation of HKU1 S was carried out based on dual-functional histidine-bonded silica (HBS) materials. The enrichment method for O-glycopeptides with HBS was developed and validated using standard proteins. The application of the developed method to the HKU1 S1 subunit resulted in 46 novel O-glycosylation sites, among which 55.6% were predicted to be exposed on the outer protein surface. Moreover, the O-linked glycans and their abundance on each HKU1 S1 site were analyzed. The obtained O-glycosylation dataset will provide valuable insights into the structure of HKU1 S.
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Affiliation(s)
- Yun Cui
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Xuefang Dong
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xiaofei Zhang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Cheng Chen
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Dongmei Fu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Xiuling Li
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xinmiao Liang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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A semi-automated, high throughput approach for O-glycosylation profiling of in vitro established cancer cell lines by MALDI-FT-ICR MS. Glycoconj J 2021; 38:747-756. [PMID: 34283362 PMCID: PMC8821499 DOI: 10.1007/s10719-021-10003-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/30/2022]
Abstract
The study of protein O-glycosylation is important in biological research as O-glycans have been reported to regulate a multitude of molecular and cell biology processes occurring in cancer. It is known that alterations in O-glycosylation are involved in the development and progression of cancer. Their easy accessibility makes in vitro established cell lines suitable and useful models for studying biological mechanisms in disease. However, the O-glycosylation analysis of large numbers of samples, as required in systems biology and biomarker discovery studies, is often challenging. In the present study, O-glycans from three human colorectal cancer cell lines and two human pancreatic cancer cell lines were released by semi-automated, high throughput reductive β-elimination and analysed using ultrahigh resolution MALDI-FT-ICR MS. Automated data integration and processing was performed using MassyTools, where the analyte was automatically included for relative quantitation based on a range of selection criteria including signal-to-noise ratio, mass error and isotopic pattern quality scores. A total of 126 O-glycan compositions, ranging from a single monosaccharide to large oligosaccharides exhibiting complex glycan motifs, were detected. The use of ultrahigh resolution MALDI-FTICR MS enabled glycan identification and quantitation in the matrix region of the spectrum. This approach has the potential to be used for O-glycosylation analysis of large numbers of samples, such as patient sample cohorts.
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Dong X, Chen C, Yan J, Zhang X, Li X, Liang X. Comprehensive O-Glycosylation Analysis of the SARS-CoV-2 Spike Protein with Biomimetic Trp-Arg Materials. Anal Chem 2021; 93:10444-10452. [PMID: 34284575 DOI: 10.1021/acs.analchem.0c04634] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a serious public health threat. Most vaccines against SARS-CoV-2 target the highly glycosylated spike protein (S). A good knowledge of the glycosylation profile of this protein is key to successful vaccine development. Unlike the 22 confirmed N-glycosylation sites on SARS-CoV-2 S, only a few O-glycosylation sites on this protein have been reported. This difference is mainly ascribed to the extremely low stoichiometry of O-glycosylation. Herein, we designed the biomimetic materials, Trp-Arg (WR) monomer-grafted silica microspheres (designated as WR-SiO2), and these biomimetic materials can enrich N- and O-linked glycopeptides with high selectivity. And WR-SiO2 can resist the nonglycopeptides' interference with the 100 molar fold of BSA during O-linked glycopeptide enrichment. We utilized WR-SiO2 to comprehensively analyze the O-glycosylation profile of recombinant SARS-CoV-2 S. Twenty-seven O-glycosylation sites including 18 unambiguous sites are identified on SARS-CoV-2 S. Our study demonstrates that the biomimetic polymer can offer specific selectivity for O-linked glycopeptides and pave the way for O-glycosylation research in biological fields. The O-glycosylation profile of SARS-CoV-2 S might supplement the comprehensive glycosylation in addition to N-glycosylation of SARS-CoV-2 S.
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Affiliation(s)
- Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jingyu Yan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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12
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Shi J, Ku X, Zou X, Hou J, Yan W, Zhang Y. Comprehensive analysis of O-glycosylation of amyloid precursor protein (APP) using targeted and multi-fragmentation MS strategy. Biochim Biophys Acta Gen Subj 2021; 1865:129954. [PMID: 34229070 DOI: 10.1016/j.bbagen.2021.129954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The aberrant proteolytic processing of amyloid precursor protein (APP) into amyloid β peptide (Aβ) in brain is a critical step in the pathogenesis of Alzheimer's disease (AD). As an O-glycosylated protein, O-glycosylation of APP is considered to be related to Aβ generation. Therefore, comprehensive analysis of APP O-glycosylation is important for understanding its functions. METHODS We developed a Targeted MS approach with Multi-Fragmentation techniques (TMMF strategy), and successfully characterized O-glycosylation profiling of APP695 expressed in HEK-293 T cells. We calculated relative abundance of glycopeptides with various O-glycosites and O-glycans, and further investigated the alteration of APP O-glycosylation upon TNF-α treatment. RESULTS A total of 14 O-glycosites were identified on three glycopeptides of APP, and at least four O-glycans including GalNAc (Tn antigen), core 1, and mono-/di-sialylated core 1 glycans were determinant at the residues of Thr576 and Thr577. We found a dense cluster of truncated O-glycans on the region nearby beginning of E2 domain and high abundance of sialylated O-glycans on the region close to β-cleavage site. Moreover, we also observed that TNF-α could upregulate the expression of APP and the truncated O-glycans on APP in HEK-293 T cell. CONCLUSION Our study established an intact O-glycopeptide MS analysis strategy for APP O-glycopeptide identification with enhanced fragmentation efficiency and detection sensitivity. These results provide a comprehensive O-glycosylation map of APP expressed in HEK-293 T cell. GENERAL SIGNIFICANCE The accurate O-glycosites and O-glycan structures on APP may lead to a better understanding of the roles O-glycosylation plays in the processing and functions of APP.
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Affiliation(s)
- Jingjing Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingli Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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13
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Hu W, Zhang R, Chen W, Lin D, Wei K, Li J, Zhang B, Li X, Tang Z. Glycosylation at Asn254 Is Required for the Activation of the PDGF-C Protein. Front Mol Biosci 2021; 8:665552. [PMID: 34109212 PMCID: PMC8181125 DOI: 10.3389/fmolb.2021.665552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Platelet-derived growth factor C (PDGF-C) is a member of the PDGF/VEGF (vascular endothelial growth factor) family, which includes proteins that are well known for their mitogenic effects on multiple cell types. Glycosylation is one of the most important forms of posttranslational modification that has a significant impact on secreted and membrane proteins. Glycosylation has many well-characterized roles in facilitating protein processing and contributes to appropriate folding, conformation, distribution, and stability of proteins that are synthesized intracellularly in the endoplasmic reticulum (ER) and Golgi apparatus. Although the general process and functions of glycosylation are well documented, there are most likely others yet to be discovered, as the glycosylation of many potential substrates has not been characterized. In this study, we report that the PDGF-C protein is glycosylated at three sites, including Asn25, Asn55, and Asn254. However, we found that mutations at any of these sites do not affect the protein expression or secretion. Similarly, disruption of PDGF-C glycosylation had no impact on its progression through the ER and Golgi apparatus. However, the introduction of a mutation at Asn254 (N254 A) prevents the activation of full-length PDGF-C and its capacity for signaling via the PDGF receptor. Our findings reveal that glycosylation affects PDGF-C activation rather than the protein synthesis or processing. This study characterizes a crucial modification of the PDGF-C protein, and may shed new light on the process and function of glycosylation.
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Affiliation(s)
- Wenjie Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Ruting Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Dongyue Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Kun Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jiahui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Bo Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Zhongshu Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
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14
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Li Z, Bin Luo, Yu L, Lan F, Wu Y. Intermolecular B-N coordination and multi-interaction synergism induced selective glycoprotein adsorption by phenylboronic acid-functionalized magnetic composites under acidic and neutral conditions. J Mater Chem B 2021; 9:453-463. [PMID: 33289778 DOI: 10.1039/d0tb01901a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abnormal protein glycosylation is associated with many diseases including cardiovascular disease, diabetes, and cancer. Therefore, selective capturing of glycoproteins under physiological or weak acid conditions (tumor microenvironment) is vital for disease diagnosis and further comprehensive analysis. Here, we propose a strategy of intermolecular B-N bond-based phenylboronic acid affinity to capture glycoproteins under neutral and slightly acidic conditions. Surprisingly, the captured glycoproteins were released in alkaline solution. This is contrary to the traditional phenylboric acid affinity, and we studied this from the perspective of materials, proteins, and incubation conditions. We identified the synergistic effect of intermolecular B-N bond-based phenylboronic acid affinity, electrostatic interaction, and polymer brush structure-based glycoprotein adsorption under slightly acidic conditions. The electrostatic repulsion between Fe3O4@SiO2@poly (2-aminoethyl methacrylate hydrochloride)-4-carboxyphenylboronic acid (Fe3O4@SiO2@PAMA-CPBA) nanoparticles and transferrin (TRF) was far greater than the specific binding between phenylboric acid of CPBA and glycosylation residues of TRF resulting in the release of the captured glycoproteins in alkaline solution. Fe3O4@SiO2@PAMA-CPBA nanoparticles exhibited different selectivity capabilities toward different glycoproteins in multiprotein solutions due to protein interactions. These results may pave a new way for the design of phenylboric acid-based materials towards glycoprotein adsorption in a physiological environment.
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Affiliation(s)
- Zhiyu Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Lingzhu Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
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15
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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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16
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Riley NM, Malaker SA, Bertozzi CR. Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis. Anal Chem 2020; 92:14878-14884. [PMID: 33125225 PMCID: PMC8329938 DOI: 10.1021/acs.analchem.0c02950] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from Akkermansia muciniphila cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans. This provides orthogonal cleavage relative to canonical proteases (e.g., trypsin) for improved O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides with a modified N-terminal residue, such as those generated by OpeRATOR, present several potential benefits, perhaps the most notable being de facto O-glycosite localization without the need of glycan-retaining fragments in MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus would enable O-glycoproteomic methods to rely solely on collision-based fragmentation rather than electron-driven dissociation because glycan-retaining peptide fragments would not be required for localization. The caveat is that modified peptides would need to reliably contain only a single O-glycosite. Here, we use methods that combine collision- and electron-based fragmentation to characterize the number of O-glycosites that are present in O-glycopeptides derived from the OpeRATOR digestion of four known O-glycoproteins. Our data show that over 50% of O-glycopeptides in our sample generated from combined digestion using OpeRATOR and trypsin contain multiple O-glycosites, indicating that collision-based fragmentation alone is not sufficient. Electron-based dissociation methods are necessary to capture the O-glycopeptide diversity present in OpeRATOR digestions.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, California, United States
| | - Stacy A Malaker
- Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, California, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, California, United States
- Howard Hughes Medical Institute, Stanford, California, United States
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17
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020. [PMID: 33106676 DOI: 10.1101/2020.05.18.102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus .
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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18
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Lu L, Riley NM, Shortreed MR, Bertozzi CR, Smith LM. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 2020; 17:1133-1138. [PMID: 33106676 PMCID: PMC7606753 DOI: 10.1038/s41592-020-00985-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
We report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at https://github.com/smith-chem-wisc/MetaMorpheus.
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Nicholas M Riley
- Department of Chemistry, University of Stanford, Stanford, CA, USA
| | | | - Carolyn R Bertozzi
- Department of Chemistry, University of Stanford, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA.
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19
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Sun J, Mu Y, Liu T, Jing H, Obadi M, Yang Y, Dong S, Xu B. Evaluation of glycation reaction of ovalbumin with dextran: Glycation sites identification by capillary liquid chromatography coupled with tandem mass spectrometry. Food Chem 2020; 341:128066. [PMID: 33035859 DOI: 10.1016/j.foodchem.2020.128066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022]
Abstract
An important relationship exists between the changes in glycation sites and structure of proteins. A combination of liquid chromatography and tandem mass spectrometry was used to identify the glycation information from ovalbumin (OVA) after dextran (Dex) conjugation under water heating (WH) or microwave heating (MH) conditions. After Dex conjugation, 12O-linked glycation sites were identified in the OVA-Dex-MH conjugates, whereas 6O-linked, 2N-linked glycation sites were detected in the OVA-Dex-WH conjugates. These findings indicate that the amino acids at different positions in OVA molecular structure have different glycation reactivity under MH or WH induction systems. In addition, β-sheet and β-turn structures showed high glycation reactivity. The increased surface hydrophobicity of OVA-Dex conjugates was possibly attributed to the glycation sites that were mainly found in hydrophilic amino acids. Our study provides useful information for the glycation mechanism research of OVA and Dex.
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Affiliation(s)
- Jun Sun
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
| | - Yaoyao Mu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Tengmei Liu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Hui Jing
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Mohammed Obadi
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Yanjun Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | | | - Bin Xu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
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20
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Affiliation(s)
- Hayden Wilkinson
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing, Research and Training, Blackrock, Dublin, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
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21
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Riley N, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. J Proteome Res 2020; 19:3286-3301. [PMID: 32500713 PMCID: PMC7425838 DOI: 10.1021/acs.jproteome.0c00218] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 01/29/2023]
Abstract
Site-specific characterization of glycosylation requires intact glycopeptide analysis, and recent efforts have focused on how to best interrogate glycopeptides using tandem mass spectrometry (MS/MS). Beam-type collisional activation, i.e., higher-energy collisional dissociation (HCD), has been a valuable approach, but stepped collision energy HCD (sceHCD) and electron transfer dissociation with HCD supplemental activation (EThcD) have emerged as potentially more suitable alternatives. Both sceHCD and EThcD have been used with success in large-scale glycoproteomic experiments, but they each incur some degree of compromise. Most progress has occurred in the area of N-glycoproteomics. There is growing interest in extending this progress to O-glycoproteomics, which necessitates comparisons of method performance for the two classes of glycopeptides. Here, we systematically explore the advantages and disadvantages of conventional HCD, sceHCD, ETD, and EThcD for intact glycopeptide analysis and determine their suitability for both N- and O-glycoproteomic applications. For N-glycopeptides, HCD and sceHCD generate similar numbers of identifications, although sceHCD generally provides higher quality spectra. Both significantly outperform EThcD methods in terms of identifications, indicating that ETD-based methods are not required for routine N-glycoproteomics even if they can generate higher quality spectra. Conversely, ETD-based methods, especially EThcD, are indispensable for site-specific analyses of O-glycopeptides. Our data show that O-glycopeptides cannot be robustly characterized with HCD-centric methods that are sufficient for N-glycopeptides, and glycoproteomic methods aiming to characterize O-glycopeptides must be constructed accordingly.
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Stacy A. Malaker
- Department
of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Marc D. Driessen
- Department
of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305-6104, United States
- Howard
Hughes Medical Institute, Stanford, California 94305-6104, United States
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22
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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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23
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Xu G, Goonatilleke E, Wongkham S, Lebrilla CB. Deep Structural Analysis and Quantitation of O-Linked Glycans on Cell Membrane Reveal High Abundances and Distinct Glycomic Profiles Associated with Cell Type and Stages of Differentiation. Anal Chem 2020; 92:3758-3768. [PMID: 32039582 DOI: 10.1021/acs.analchem.9b05103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proteins on cell membrane are modified by N- and O-glycans. N-Glycans have been extensively characterized using advanced separation and mass spectrometry techniques. However, O-glycans remain a challenge, because of the lack of universal enzymes to release them and the large background abundances of N-glycans. Here, we report a method for in-depth structural analysis and quantitation of O-glycans derived from human cell membrane. O-Glycans were chemically released from isolated cell membrane glycoproteins following N-glycan and lipid/glycolipid removal by PNGase F digestion and Folch extraction, respectively. Released O-glycans were purified by an optimized protocol to eliminate interference from small molecules and degraded proteins. Cell surface O-glycans were then analyzed using a nanoLC-chip-QTOF mass spectrometer with a porous graphitized carbon (PGC) column, while the N-glycans and glycolipids isolated from the same cell membrane fractions were analyzed in parallel using previously reported methods. The monosaccharide compositions and linkages of the detected O-glycans were identified by exoglycosidase digestion facilitated with tandem mass spectrometry (MS/MS). Using this method, we identified 44 cell membrane O-glycan isomers with MS/MS, and, among them, we unambiguously characterized 25 O-glycan structures with exoglycosidase digestion to create a library with their complete structures, accurate masses, and retention times. In this process, we identified and characterized unexpected mannose oligomers that are α(1-2/3) linked. This library enabled the identification and quantification of unique cell surface O-glycans from different cell lines and the study of specific O-glycan changes during cell differentiation.
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Affiliation(s)
- Gege Xu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, California 95616, 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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Zhu H, Aloor A, Ma C, Kondengaden SM, Wang PG. Mass Spectrometric Analysis of Protein Glycosylation. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1346.ch010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- He Zhu
- These authors contributed equally
| | | | | | | | - Peng George Wang
- Current Address: Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
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26
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Li Q, Xie Y, Wong M, Lebrilla CB. Characterization of Cell Glycocalyx with Mass Spectrometry Methods. Cells 2019; 8:E882. [PMID: 31412618 PMCID: PMC6721671 DOI: 10.3390/cells8080882] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, University of California, Davis, CA 95616, USA.
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27
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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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 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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28
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Mao J, You X, Qin H, Wang C, Wang L, Ye M. A New Searching Strategy for the Identification of O-Linked Glycopeptides. Anal Chem 2019; 91:3852-3859. [PMID: 30802037 DOI: 10.1021/acs.analchem.8b04184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
For the analysis of homogeneous post-translational modifications such as protein phosphorylation and acetylation, setting a variable modification on the specific residue(s) is applied to identify the modified peptides for database searching. However, this approach is often not applicable to identify intact mucin-type O-glycopeptides due to the high microheterogeneity of the glycosylation. Because there is virtually no carbohydrate-related tag on the peptide fragments after the O-glycopeptides are dissociated in HCD, we find it is unnecessary to set the variable mass tags on the Ser/Thr residues to identify the peptide sequences. In this study, we present a novel approach, termed as O-Search, for the interpretation of O-glycopeptide HCD spectra. Instead of setting the variable mass tags on the Ser/Thr residues, we set variable mass tags on the peptide level. The precursor mass of the MS/MS spectrum was deducted by every possible summed mass of O-glycan combinations on at most three S/T residues. All the spectra with these new precursor masses were searched against the protein sequence database without setting variable glycan modifications. It was found that this method had much decreased search space and had excellent sensitivity in the identification of O-glycopeptides. Compared with the conventional searching approach, O-Search yielded 96%, 86%, and 79% improvement in glycopeptide spectra matching, glycopeptide identification, and peptide sequence identification, respectively. It was demonstrated that O-Search enabled the consideration of more glycan structures and was fitted to analyze microheterogeneity of O-glycosylation.
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Affiliation(s)
- Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Science , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xin You
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Science , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Science , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chengye Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery , The Second Hospital of Dalian Medical University , Dalian , Liaoning 116023 , China
| | - Liming Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery , The Second Hospital of Dalian Medical University , Dalian , Liaoning 116023 , China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Science , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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Kotsias M, Kozak RP, Gardner RA, Wuhrer M, Spencer DIR. Improved and semi-automated reductive β-elimination workflow for higher throughput protein O-glycosylation analysis. PLoS One 2019; 14:e0210759. [PMID: 30653606 PMCID: PMC6336230 DOI: 10.1371/journal.pone.0210759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/01/2019] [Indexed: 11/19/2022] Open
Abstract
Protein O-glycosylation has shown to be critical for a wide range of biological processes, resulting in an increased interest in studying the alterations in O-glycosylation patterns of biological samples as disease biomarkers as well as for patient stratification and personalized medicine. Given the complexity of O-glycans, often a large number of samples have to be analysed in order to obtain conclusive results. However, most of the O-glycan analysis work done so far has been performed using glycoanalytical technologies that would not be suitable for the analysis of large sample sets, mainly due to limitations in sample throughput and affordability of the methods. Here we report a largely automated system for O-glycan analysis. We adapted reductive β-elimination release of O-glycans to a 96-well plate system and transferred the protocol onto a liquid handling robot. The workflow includes O-glycan release, purification and derivatization through permethylation followed by MALDI-TOF-MS. The method has been validated according to the ICH Q2 (R1) guidelines for the validation of analytical procedures. The semi-automated reductive β-elimination system enabled for the characterization and relative quantitation of O-glycans from commercially available standards. Results of the semi-automated method were in good agreement with the conventional manual in-solution method while even outperforming it in terms of repeatability. Release of O-glycans for 96 samples was achieved within 2.5 hours, and the automated data acquisition on MALDI-TOF-MS took less than 1 minute per sample. This largely automated workflow for O-glycosylation analysis showed to produce rapid, accurate and reliable data, and has the potential to be applied for O-glycan characterization of biological samples, biopharmaceuticals as well as for biomarker discovery.
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Affiliation(s)
| | - Radoslaw P. Kozak
- Ludger Ltd, Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Richard A. Gardner
- Ludger Ltd, Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Manfred Wuhrer
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, Netherlands
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Nan L, Li J, Jin W, Wei M, Tang M, Wang C, Gong G, Huang L, Zhang Y, Wang Z. Comprehensive quali-quantitative profiling of neutral and sialylated O-glycome by mass spectrometry based on oligosaccharide metabolic engineering and isotopic labeling. RSC Adv 2019; 9:15694-15702. [PMID: 35521403 PMCID: PMC9064288 DOI: 10.1039/c9ra01114e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/11/2019] [Indexed: 01/26/2023] Open
Abstract
An isotopic precursor based metabolic amplification and labeling (IPMAL) strategy using the Ac3GalNAc-α-Bn precursor to simultaneously quantify neutral and sialylated O-glycans.
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31
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Peng JX, He PP, Wei PY, Zhang B, Zhao YZ, Li QY, Chen XL, Peng M, Zeng DG, Yang CL, Chen X. Proteomic Responses Under Cold Stress Reveal Unique Cold Tolerance Mechanisms in the Pacific White Shrimp ( Litopenaeus vannamei). Front Physiol 2018; 9:1399. [PMID: 30483139 PMCID: PMC6243039 DOI: 10.3389/fphys.2018.01399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/13/2018] [Indexed: 11/13/2022] Open
Abstract
The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, often suffers from cold stress. To understand the molecular mechanism of cold tolerance in Pacific white shrimp, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, cold-tolerant Guihai2 (GH2) and cold-sensitive Guihai1 (GH1), under normal temperature (28°C), under cold stress (16°C), and during recovery to 28°C. In total, 3,349 proteins were identified, among which 2,736 proteins were quantified. Based on gene ontology annotations, differentially expressed proteins largely belonged to biological processes, cellular components, and molecular functions. KEGG pathway annotations indicated that the main changes were observed in the lysosome, ribosomes, and oxidative phosphorylation. Subcellular localization analysis showed a significant increase in proteins present in cytosol, extracellular regions, and mitochondria. Combining enrichment-based clustering analysis and qRT-PCR analysis, we found that glutathione S-transferase, zinc proteinase, m7GpppX diphosphatase, AP2 transcription complex, and zinc-finger transcription factors played a major role in the cold stress response in Pacific white shrimp. Moreover, structure proteins, including different types of lectin and DAPPUDRAFT, were indispensable for cold stress tolerance of the Pacific white shrimp. Results indicate the molecular mechanisms of the Pacific white shrimp in response to cold stress and provide new insight into breeding new cultivars with increased cold tolerance.
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Affiliation(s)
- Jin-Xia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Ping-Ping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pin-Yuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yong-Zhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiang-Yong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiu-Li Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Di-Gang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chun-Ling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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32
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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33
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Laarse SAM, Leney AC, Heck AJR. Crosstalk between phosphorylation and O‐Glc
NA
cylation: friend or foe. FEBS J 2018; 285:3152-3167. [DOI: 10.1111/febs.14491] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Saar A. M. Laarse
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
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Dziurkowska E, Wesolowski M. Evaluation of solid-phase extraction procedures for the quantitation of venlafaxine in human saliva by high-performance liquid chromatography. J Sep Sci 2018; 41:2151-2160. [DOI: 10.1002/jssc.201701184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Ewelina Dziurkowska
- Department of Analytical Chemistry; Medical University of Gdansk; Gdansk Poland
| | - Marek Wesolowski
- Department of Analytical Chemistry; Medical University of Gdansk; Gdansk Poland
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