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Kim A, Kim J, Park CS, Jin M, Kang M, Moon C, Kim M, Kim J, Yang S, Jang L, Jang JY, Kim HH. Peptide-N-glycosidase F or A treatment and procainamide-labeling for identification and quantification of N-glycans in two types of mammalian glycoproteins using UPLC and LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123538. [PMID: 36493594 DOI: 10.1016/j.jchromb.2022.123538] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND N-glycans in glycoproteins can affect physicochemical properties of proteins; however, some reported N-glycan structures are inconsistent depending on the type of glycoprotein or the preparation methods. OBJECTIVE To obtain consistent results for qualitative and quantitative analyses of N-glycans, N-glycans obtained by different preparation methods were compared for two types of mammalian glycoproteins. METHODS N-glycans are released by peptide-N-glycosidase F (PF) or A (PA) from two model mammalian glycoproteins, bovine fetuin (with three glycosylation sites) and human IgG (with a single glycosylation site), and labeled with a fluorescent tag [2-aminobenzamide (AB) or procainamide (ProA)]. The structure and quantity of each N-glycan were determined using UPLC and LC-MS/MS. RESULTS The 21 N-glycans in fetuin and another 21 N-glycans in IgG by either PF-ProA or PA-ProA were identified using LC-MS/MS. The N-glycans in fetuin (8-13 N-glycans were previously reported) and in IgG (19 N-glycans were previously reported), which could not be identified by using the widely used PF-AB, were all identified by using PF-ProA or PA-ProA. The quantities (%) of the N-glycans (>0.1 %) relative to the total amount of N-glycans (100 %) obtained by AB- and ProA-labeling using LC-MS/MS had a similar tendency. However, the absolute quantities (pmol) of the N-glycans estimated using UPLC and LC-MS/MS were more efficiently determined with ProA-labeling than with AB-labeling. Thus, PF-ProA or PA-ProA allows for more effective identification and quantification of N-glycans than PF-AB in glycoprotein, particularly bovine fetuin. This study is the first comparative analysis for the identification and relative and absolute quantification of N-glycans in glycoproteins with PF-ProA and PA-ProA using UPLC and LC-MS/MS.
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Affiliation(s)
- Ahyeon Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jeongeun Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chi Soo Park
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Mijung Jin
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Minju Kang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chulmin Moon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Mirae Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jieun Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Subin Yang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Leeseul Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ji Yeon Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
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Baboo S, Diedrich JK, Martínez-Bartolomé S, Wang X, Schiffner T, Groschel B, Schief WR, Paulson JC, Yates JR. DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. Methods Enzymol 2022; 682:137-185. [PMID: 36948700 PMCID: PMC11032187 DOI: 10.1016/bs.mie.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditional mass spectrometry-based glycoproteomic approaches have been widely used for site-specific N-glycoform analysis, but a large amount of starting material is needed to obtain sampling that is representative of the vast diversity of N-glycans on glycoproteins. These methods also often include a complicated workflow and very challenging data analysis. These limitations have prevented glycoproteomics from being adapted to high-throughput platforms, and the sensitivity of the analysis is currently inadequate for elucidating N-glycan heterogeneity in clinical samples. Heavily glycosylated spike proteins of enveloped viruses, recombinantly expressed as potential vaccines, are prime targets for glycoproteomic analysis. Since the immunogenicity of spike proteins may be impacted by their glycosylation patterns, site-specific analysis of N-glycoforms provides critical information for vaccine design. Using recombinantly expressed soluble HIV Env trimer, we describe DeGlyPHER, a modification of our previously reported sequential deglycosylation strategy to yield a "single-pot" process. DeGlyPHER is an ultrasensitive, simple, rapid, robust, and efficient approach for site-specific analysis of protein N-glycoforms, that we developed for analysis of limited quantities of glycoproteins.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
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Guo R, Zhang T, Lambert TOT, Wang T, Voglmeir J, Rand KD, Liu L. PNGase H + variant from Rudaea cellulosilytica with improved deglycosylation efficiency for rapid analysis of eukaryotic N-glycans and hydrogen deuterium exchange mass spectrometry analysis of glycoproteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9376. [PMID: 35945033 PMCID: PMC9541014 DOI: 10.1002/rcm.9376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The analysis of glycoproteins and the comparison of protein N-glycosylation from different eukaryotic origins require unbiased and robust analytical workflows. The structural and functional analysis of vertebrate protein N-glycosylation currently depends extensively on bacterial peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidases (PNGases), which are indispensable enzymatic tools in releasing asparagine-linked oligosaccharides (N-glycans) from glycoproteins. So far, only limited PNGase candidates are available for N-glycans analysis, and particularly the analysis of plant and invertebrate N-glycans is hampered by the lack of suitable PNGases. Furthermore, liquid chromatography-mass spectrometry (LC-MS) workflows, such as hydrogen deuterium exchange mass spectrometry (HDX-MS), require a highly efficient enzymatic release of N-glycans at low pH values to facilitate the comprehensive structural analysis of glycoproteins. Herein, we describe a previously unstudied superacidic bacterial N-glycanase (PNGase H+ ) originating from the soil bacterium Rudaea cellulosilytica (Rc), which has significantly improved enzymatic properties compared to previously described PNGase H+ variants. Active and soluble recombinant PNGase Rc was expressed at a higher protein level (3.8-fold) and with higher specific activity (~56% increase) compared to the currently used PNGase H+ variant from Dyella japonicum (Dj). Recombinant PNGase Rc was able to deglycosylate the glycoproteins horseradish peroxidase and bovine lactoferrin significantly faster than PNGase Dj (10 min vs. 6 h). The versatility of PNGase Rc was demonstrated by releasing N-glycans from a diverse array of samples such as peach fruit, king trumpet mushroom, mouse serum, and the soil nematode Caenorhabditis elegans. The presence of only two disulfide bonds shown in the AlphaFold protein model (so far all other superacidic PNGases possess more disulfide bonds) could be corroborated by intact mass- and peptide mapping analysis and provides a possible explanation for the improved recombinant expression yield of PNGase Rc.
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Affiliation(s)
- Rui‐Rui Guo
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Tian‐Chan Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | | | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Kasper D. Rand
- Protein Analysis Group, Department of PharmacyUniversity of CopenhagenCopenhagenDenmark
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
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Liew CY, Chen JL, Tsai ST, Ni CK. Identification of side-reaction products generated during the ammonia-catalyzed release of N-glycans. Carbohydr Res 2022; 522:108686. [DOI: 10.1016/j.carres.2022.108686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022]
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Veličković D, Liao YC, Thibert S, Veličković M, Anderton C, Voglmeir J, Stacey G, Zhou M. Spatial Mapping of Plant N-Glycosylation Cellular Heterogeneity Inside Soybean Root Nodules Provided Insights Into Legume-Rhizobia Symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:869281. [PMID: 35651768 PMCID: PMC9150855 DOI: 10.3389/fpls.2022.869281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Although ubiquitously present, information on the function of complex N-glycan posttranslational modification in plants is very limited and is often neglected. In this work, we adopted an enzyme-assisted matrix-assisted laser desorption/ionization mass spectrometry imaging strategy to visualize the distribution and identity of N-glycans in soybean root nodules at a cellular resolution. We additionally performed proteomics analysis to probe the potential correlation to proteome changes during symbiotic rhizobia-legume interactions. Our ion images reveal that intense N-glycosylation occurs in the sclerenchyma layer, and inside the infected cells within the infection zone, while morphological structures such as the cortex, uninfected cells, and cells that form the attachment with the root are fewer N-glycosylated. Notably, we observed different N-glycan profiles between soybean root nodules infected with wild-type rhizobia and those infected with mutant rhizobia incapable of efficiently fixing atmospheric nitrogen. The majority of complex N-glycan structures, particularly those with characteristic Lewis-a epitopes, are more abundant in the mutant nodules. Our proteomic results revealed that these glycans likely originated from proteins that maintain the redox balance crucial for proper nitrogen fixation, but also from enzymes involved in N-glycan and phenylpropanoid biosynthesis. These findings indicate the possible involvement of Lewis-a glycans in these critical pathways during legume-rhizobia symbiosis.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yen-Chen Liao
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marija Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Christopher Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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6
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Uehara I, Kajita M, Tanimura A, Hida S, Onda M, Naito Z, Taki S, Tanaka N. 2-Deoxy-d-glucose induces deglycosylation of proinflammatory cytokine receptors and strongly reduces immunological responses in mouse models of inflammation. Pharmacol Res Perspect 2022; 10:e00940. [PMID: 35212163 PMCID: PMC8873284 DOI: 10.1002/prp2.940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
Anti‐proinflammatory cytokine therapies against interleukin (IL)‐6, tumor necrosis factor (TNF)‐α, and IL‐1 are major advancements in treating inflammatory diseases, especially rheumatoid arthritis. Such therapies are mainly performed by injection of antibodies against cytokines or cytokine receptors. We initially found that the glycolytic inhibitor 2‐deoxy‐d‐glucose (2‐DG), a simple monosaccharide, attenuated cellular responses to IL‐6 by inhibiting N‐linked glycosylation of the IL‐6 receptor gp130. Aglycoforms of gp130 did not bind to IL‐6 or activate downstream intracellular signals that included Janus kinases. 2‐DG completely inhibited dextran sodium sulfate‐induced colitis, a mouse model for inflammatory bowel disease, and alleviated laminarin‐induced arthritis in the SKG mouse, an experimental model for human rheumatoid arthritis. These diseases have been shown to be partially dependent on IL‐6. We also found that 2‐DG inhibited signals for other proinflammatory cytokines such as TNF‐α, IL‐1β, and interferon ‐γ, and accordingly, prevented death by another inflammatory disease, lipopolysaccharide (LPS) shock. Furthermore, 2‐DG prevented LPS shock, a model for a cytokine storm, and LPS‐induced pulmonary inflammation, a model for acute respiratory distress syndrome of coronavirus disease 2019 (COVID‐19). These results suggest that targeted therapies that inhibit cytokine receptor glycosylation are effective for treatment of various inflammatory diseases.
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Affiliation(s)
- Ikuno Uehara
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Mitsuko Kajita
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Atsuko Tanimura
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigeaki Hida
- Department of Molecular and Cellular Health Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Munehiko Onda
- Department of Pathology, Integrative Oncological Pathology, Nippon Medical School, Tokyo, Japan
| | - Zenya Naito
- Department of Pathology, Integrative Oncological Pathology, Nippon Medical School, Tokyo, Japan
| | - Shinsuke Taki
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Nobuyuki Tanaka
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
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7
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Baboo S, Diedrich JK, Martínez-Bartolomé S, Wang X, Schiffner T, Groschel B, Schief WR, Paulson JC, Yates JR. DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike N-Glycoforms. Anal Chem 2021; 93:13651-13657. [PMID: 34597027 DOI: 10.1021/acs.analchem.1c03059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses can evade the host immune system by displaying numerous glycans on their surface "spike-proteins" that cover immune epitopes. We have developed an ultrasensitive "single-pot" method to assess glycan occupancy and the extent of glycan processing from high-mannose to complex forms at each N-glycosylation site. Though aimed at characterizing glycosylation of viral spike-proteins as potential vaccines, this method is applicable for the analysis of site-specific glycosylation of any glycoprotein.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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Abstract
Tissue glycans usually contain various structures, from simple to highly complicated, in different quantities. N-Glycans are particularly heterogeneous, with up to pentaantennary structures, different branch sequences, and several isomeric structures. 2-Aminopyridine (PA) tagging on released N-glycans is useful for separating isomers and to quantitatively analyze both the major and minor glycan structures in tissues using reversed-phase liquid chromatography (LC)-mass spectrometry (MS) and MS/MS analysis. Because the structural differences of PA-N-glycans influence their retention on a reversed-phase C18 column, it is easy to deduce the core structure, including core Fuc and bisecting GlcNAc as well as the branching pattern of each PA-N-glycan, based on the results of elution position, full MS, and MS/MS analysis. If more detailed structural analysis is required, combining sequential exoglycosidase digestions, sialic acid linkage-specific alkylamidation (SALSA), and/or SALSA/permethylation is useful for determining glycosidic linkages of branches. This article includes detailed protocols for the preparation of N-glycans released from glycoproteins/glycopeptides by glycoamidase F or hydrazinolysis, PA-tagging of N-glycans, fractionation with anion-exchange chromatography, and chemical or enzymatic modifications of PA-N-glycans, as well as reversed-phase LC-MS, MS/MS, and MSn analysis of PA-N-glycans from tissues. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of released N-glycans from tissue samples using glycoamidase F Alternate Protocol: Preparation of released N-glycans from tissue samples by hydrazinolysis Basic Protocol 2: PA-tagging of N-glycans and sample cleanup Support Protocol 1: Monitoring of PA-N-glycans using normal-phase HPLC Basic Protocol 3: Anion-exchange chromatography of PA-N-glycans Basic Protocol 4: Sequential exoglycosidase digestions Basic Protocol 5: Determination of Sia-linkages by SALSA Support Protocol 2: Cotton-HILIC solid-phase extraction to remove reagents for alkylamidation Basic Protocol 6: Sequential modifications of glycans with SALSA and permethylation Basic Protocol 7: LC-MS and MS/MS analysis of PA-N-glycans (before permethylation) Basic Protocol 8: LC-MS, MS/MS, and MSn analysis of PA-N-glycans (after permethylation).
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Affiliation(s)
- Noriko Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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Petrović T, Trbojević-Akmačić I. Lectin and Liquid Chromatography-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:29-72. [PMID: 34687007 DOI: 10.1007/978-3-030-76912-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunoglobulin (Ig) glycosylation has been shown to dramatically affect its structure and effector functions. Ig glycosylation changes have been associated with different diseases and show a promising biomarker potential for diagnosis and prognosis of disease advancement. On the other hand, therapeutic biomolecules based on structural and functional features of Igs demand stringent quality control during the production process to ensure their safety and efficacy. Liquid chromatography (LC) and lectin-based methods are routinely used in Ig glycosylation analysis complementary to other analytical methods, e.g., mass spectrometry and capillary electrophoresis. This chapter covers analytical approaches based on LC and lectins used in low- and high-throughput N- and O-glycosylation analysis of Igs, with the focus on immunoglobulin G (IgG) applications. General principles and practical examples of the most often used LC methods for Ig purification are described, together with typical workflows for N- and O-glycan analysis on the level of free glycans, glycopeptides, subunits, or intact Igs. Lectin chromatography is a historical approach for the analysis of lectin-carbohydrate interactions and glycoprotein purification but is still being used as a valuable tool in Igs purification and glycan analysis. On the other hand, lectin microarrays have found their application in the rapid screening of glycan profiles on intact proteins.
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Affiliation(s)
- Tea Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
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Unique Microbial Catabolic Pathway for the Human Core N-Glycan Constituent Fucosyl-α-1,6- N-Acetylglucosamine-Asparagine. mBio 2020; 11:mBio.02804-19. [PMID: 31937642 PMCID: PMC6960285 DOI: 10.1128/mbio.02804-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The gastrointestinal tract accommodates more than 1014 microorganisms that have an enormous impact on human health. The mechanisms enabling commensal bacteria and administered probiotics to colonize the gut remain largely unknown. The ability to utilize host-derived carbon and energy resources available at the mucosal surfaces may provide these bacteria with a competitive advantage in the gut. Here, we have identified in the commensal species Lactobacillus casei a novel metabolic pathway for the utilization of the glycoamino acid fucosyl-α-1,6-N-GlcNAc-Asn, which is present in the core-fucosylated N-glycoproteins from mammalians. These results give insight into the molecular interactions between the host and commensal/probiotic bacteria and may help to devise new strategies to restore gut microbiota homeostasis in diseases associated with dysbiotic microbiota. The survival of commensal bacteria in the human gut partially depends on their ability to metabolize host-derived molecules. The use of the glycosidic moiety of N-glycoproteins by bacteria has been reported, but the role of N-glycopeptides or glycoamino acids as the substrates for bacterial growth has not been evaluated. We have identified in Lactobacillus casei strain BL23 a gene cluster (alf-2) involved in the catabolism of the glycoamino acid fucosyl-α-1,6-N-GlcNAc-Asn (6′FN-Asn), a constituent of the core-fucosylated structures of mammalian N-glycoproteins. The cluster consists of the genes alfHC, encoding a major facilitator superfamily (MFS) permease and the α-l-fucosidase AlfC, and the divergently oriented asdA (aspartate 4-decarboxylase), alfR2 (transcriptional regulator), pepV (peptidase), asnA2 (glycosyl-asparaginase), and sugK (sugar kinase) genes. Knockout mutants showed that alfH, alfC, asdA, asnA2, and sugK are necessary for efficient 6′FN-Asn utilization. The alf-2 genes are induced by 6′FN-Asn, but not by its glycan moiety, via the AlfR2 regulator. The constitutive expression of alf-2 genes in an alfR2 strain allowed the metabolism of a variety of 6′-fucosyl-glycans. However, GlcNAc-Asn did not support growth in this mutant background, indicating that the presence of a 6′-fucose moiety is crucial for substrate transport via AlfH. Within bacteria, 6′FN-Asn is defucosylated by AlfC, generating GlcNAc-Asn. This glycoamino acid is processed by the glycosylasparaginase AsnA2. GlcNAc-Asn hydrolysis generates aspartate and GlcNAc, which is used as a fermentable source by L.casei. These data establish the existence in a commensal bacterial species of an exclusive metabolic pathway likely to scavenge human milk and mucosal fucosylated N-glycopeptides in the gastrointestinal tract.
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11
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Direct Addition of Amides to Glycals Enabled by Solvation‐Insusceptible 2‐Haloazolium Salt Catalysis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Nakatsuji Y, Kobayashi Y, Takemoto Y. Direct Addition of Amides to Glycals Enabled by Solvation-Insusceptible 2-Haloazolium Salt Catalysis. Angew Chem Int Ed Engl 2019; 58:14115-14119. [PMID: 31392793 DOI: 10.1002/anie.201907129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/24/2019] [Indexed: 01/12/2023]
Abstract
The direct 2-deoxyglycosylation of nucleophiles with glycals leads to biologically and pharmacologically important 2-deoxysugar compounds. Although the direct addition of hydroxyl and sulfonamide groups have been well developed, the direct 2-deoxyglycosylation of amide groups has not been reported to date. Herein, we show the first direct 2-deoxyglycosylation of amide groups using a newly designed Brønsted acid catalyst under mild conditions. Through mechanistic investigations, we discovered that the amide group can inhibit acid catalysts, and the inhibition has made the 2-deoxyglycosylation reaction difficult. Diffusion-ordered two-dimensional NMR spectroscopy analysis implied that the 2-chloroazolium salt catalyst was less likely to form aggregates with amides in comparison to other acid catalysts. The chlorine atom and the extended π-scaffold of the catalyst played a crucial role for this phenomenon. This relative insusceptibility to inhibition by amides is more responsible for the catalytic activity than the strength of the acidity.
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Affiliation(s)
- Yuya Nakatsuji
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yusuke Kobayashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
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13
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Gao C, Hanes MS, Byrd-Leotis LA, Wei M, Jia N, Kardish RJ, McKitrick TR, Steinhauer DA, Cummings RD. Unique Binding Specificities of Proteins toward Isomeric Asparagine-Linked Glycans. Cell Chem Biol 2019; 26:535-547.e4. [PMID: 30745240 DOI: 10.1016/j.chembiol.2019.01.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/18/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
The glycan ligands recognized by Siglecs, influenza viruses, and galectins, as well as many plant lectins, are not well defined. To explore their binding to asparagine (Asn)-linked N-glycans, we synthesized a library of isomeric multiantennary N-glycans that vary in terminal non-reducing sialic acid, galactose, and N-acetylglucosamine residues, as well as core fucose. We identified specific recognition of N-glycans by several plant lectins, human galectins, influenza viruses, and Siglecs, and explored the influence of sialic acid linkages and branching of the N-glycans. These results show the unique recognition of complex-type N-glycans by a wide variety of glycan-binding proteins and their abilities to distinguish isomeric structures, which provides new insights into the biological roles of these proteins and the uses of lectins in biological applications to identify glycans.
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Affiliation(s)
- Chao Gao
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Melinda S Hanes
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Lauren A Byrd-Leotis
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA; Department of Microbiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Mohui Wei
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Nan Jia
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Robert J Kardish
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Tanya R McKitrick
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - David A Steinhauer
- Department of Microbiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA.
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14
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Abstract
Glycosylation, one of the most frequent protein posttranslational modifications, is involved in the mechanisms of cell-cell interactions and immune reactions and is modulated in the course of diseases. In contrary to chemical glycan release, enzymatic cleavage of N-glycans can be performed in any laboratory with relative ease. We present here two robust protocols to achieve N-glycan release. The first one uses trypsin to disrupt protein structure whereas the other involves the use of detergents prior to PNGase F digestion. Thereafter, N-glycans are isolated from peptides using reverse-phase cartridges and are desalted with carbograph cartridges before finally being derivatized with the fluorescent label 2AB.
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Affiliation(s)
- Detlef Grunow
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
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15
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Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
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Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
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16
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Du YM, Zheng SL, Liu L, Voglmeir J, Yedid G. Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H. J Vis Exp 2018. [PMID: 29985337 DOI: 10.3791/57979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In recent years, the carbohydrate moieties of plants have received considerable attention, as they are a potential source of cross-reactive, allergy-provoking immune responses. In addition, carbohydrate structures also play a critical role in plant metabolism. Here, we present a simple and rapid method for preparing and analyzing N-glycans from different cultivars of radish (Raphanus sativus) using an N-glycanase specific for the release of plant-derived carbohydrate structures. To achieve this, crude trichloroacetic acid precipitates of radish homogenates were treated with PNGase H+, and labeled using 2-aminobenzamide as a fluorescent tag. The labeled N-glycan samples were subsequently analyzed by ultra performance liquid chromatography (UPLC) separation and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for a detailed structural evaluation and to quantify relative abundancies of the radish-derived N-glycan structures. This protocol can also be used for the analysis of N-glycans from various other plant species, and may be useful for further investigation of the function and effects of N-glycans on human health.
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Affiliation(s)
- Ya-Min Du
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University
| | - Shen-Li Zheng
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University;
| | - Gabriel Yedid
- College of Life Science, Nanjing Agricultural University;
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17
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Briggs MT, Ho YY, Kaur G, Oehler MK, Everest-Dass AV, Packer NH, Hoffmann P. N-Glycan matrix-assisted laser desorption/ionization mass spectrometry imaging protocol for formalin-fixed paraffin-embedded tissues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:825-841. [PMID: 28271569 DOI: 10.1002/rcm.7845] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) of the proteome of a tissue has been an established technique for the past decade. In the last few years, MALDI-MSI of the N-glycome has emerged as a novel MALDI-MSI technique. To assess the accuracy and clinical significance of the N-linked glycan spatial distribution, we have developed a method that utilises MALDI-MSI followed by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) in order to assign glycan structures to the differentiating MALDI-MSI glycan masses released from the tissue glycoproteins. METHODS AND RESULTS Our workflow presents a comprehensive list of instructions on how to (i) apply MALDI-MSI to spatially map the N-glycome across formalin-fixed paraffin-embedded (FFPE) clinical samples, (ii) structurally characterise N-glycans extracted from consecutive FFPE tissue sections by LC/MS/MS, and (iii) match relevant N-glycan masses from MALDI-MSI with confirmed N-glycan structures determined by LC/MS/MS. CONCLUSIONS Our protocol provides groups that are new to this technique with instructions how to establish N-glycan MALDI-MSI in their laboratory. Furthermore, the method assigns N-glycan structural detail to the masses obtained in the MALDI-MS image. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Matthew T Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia, 5005
| | - Yin Ying Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Martin K Oehler
- Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, 5005, Australia
- Robinson Institute, University of Adelaide, Adelaide, Australia, 5005
| | - Arun V Everest-Dass
- ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, Australia, 5005
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, 2109
| | - Nicolle H Packer
- ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, Australia, 5005
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, 2109
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, Australia, 5005
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia, 5005
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18
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Jensen PF, Comamala G, Trelle MB, Madsen JB, Jørgensen TJD, Rand KD. Removal of N-Linked Glycosylations at Acidic pH by PNGase A Facilitates Hydrogen/Deuterium Exchange Mass Spectrometry Analysis of N-Linked Glycoproteins. Anal Chem 2016; 88:12479-12488. [DOI: 10.1021/acs.analchem.6b03951] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pernille Foged Jensen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Gerard Comamala
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Morten Beck Trelle
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jeppe Buur Madsen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kasper. D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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19
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Song X, Ju H, Lasanajak Y, Kudelka MR, Smith DF, Cummings RD. Oxidative release of natural glycans for functional glycomics. Nat Methods 2016; 13:528-34. [PMID: 27135973 PMCID: PMC4887297 DOI: 10.1038/nmeth.3861] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/28/2016] [Indexed: 12/13/2022]
Abstract
Glycans have essential roles in biology and the etiology of many diseases. A major hurdle in studying glycans through functional glycomics is the lack of methods to release glycans from diverse types of biological samples. Here we describe an oxidative strategy using household bleach to release all types of free reducing N-glycans and O-glycan-acids from glycoproteins, and glycan nitriles from glycosphingolipids. Released glycans are directly useful in glycomic analyses and can be derivatized fluorescently for functional glycomics. This chemical method overcomes the limitations in glycan generation and promotes archiving and characterization of human and animal glycomes and their functions.
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Affiliation(s)
- Xuezheng Song
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hong Ju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yi Lasanajak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Matthew R Kudelka
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David F Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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20
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Zhou S, Tello N, Harvey A, Boyes B, Orlando R, Mechref Y. Reliable LC-MS quantitative glycomics using iGlycoMab stable isotope labeled glycans as internal standards. Electrophoresis 2016; 37:1489-97. [PMID: 26913967 PMCID: PMC4964797 DOI: 10.1002/elps.201600013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 01/09/2023]
Abstract
Glycans have numerous functions in various biological processes and participate in the progress of diseases. Reliable quantitative glycomic profiling techniques could contribute to the understanding of the biological functions of glycans, and lead to the discovery of potential glycan biomarkers for diseases. Although LC-MS is a powerful analytical tool for quantitative glycomics, the variation of ionization efficiency and MS intensity bias are influencing quantitation reliability. Internal standards can be utilized for glycomic quantitation by MS-based methods to reduce variability. In this study, we used stable isotope labeled IgG2b monoclonal antibody, iGlycoMab, as an internal standard to reduce potential for errors and to reduce variabililty due to sample digestion, derivatization, and fluctuation of nanoESI efficiency in the LC-MS analysis of permethylated N-glycans released from model glycoproteins, human blood serum, and breast cancer cell line. We observed an unanticipated degradation of isotope labeled glycans, tracked a source of such degradation, and optimized a sample preparation protocol to minimize degradation of the internal standard glycans. All results indicated the effectiveness of using iGlycoMab to minimize errors originating from sample handling and instruments.
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Affiliation(s)
- Shiyue Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Nadia Tello
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
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21
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Zhang X. Instant Integrated Ultradeep Quantitative-structural Membrane Proteomics Discovered Post-translational Modification Signatures for Human Cys-loop Receptor Subunit Bias. Mol Cell Proteomics 2016; 15:3665-3684. [PMID: 27073180 DOI: 10.1074/mcp.m114.047514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 11/17/2015] [Indexed: 12/31/2022] Open
Abstract
Neurotransmitter ligand-gated ion channels (LGICs) are widespread and pivotal in brain functions. Unveiling their structure-function mechanisms is crucial to drive drug discovery, and demands robust proteomic quantitation of expression, post-translational modifications (PTMs) and dynamic structures. Yet unbiased digestion of these modified transmembrane proteins-at high efficiency and peptide reproducibility-poses the obstacle. Targeting both enzyme-substrate contacts and PTMs for peptide formation and detection, we devised flow-and-detergent-facilitated protease and de-PTM digestions for deep sequencing (FDD) method that combined omni-compatible detergent, tandem immobilized protease/PNGase columns, and Cys-selective reduction/alkylation, to achieve streamlined ultradeep peptide preparation within minutes not days, at high peptide reproducibility and low abundance-bias. FDD transformed enzyme-protein contacts into equal catalytic travel paths through enzyme-excessive columns regardless of protein abundance, removed products instantly preventing inhibition, tackled intricate structures via sequential multiple micro-digestions along the flow, and precisely controlled peptide formation by flow rate. Peptide-stage reactions reduced steric bias; low contamination deepened MS/MS scan; distinguishing disulfide from M oxidation and avoiding gain/loss artifacts unmasked protein-endogenous oxidation states. Using a recent interactome of 285-kDa human GABA type A receptor, this pilot study validated FDD platform's applicability to deep sequencing (up to 99% coverage), H/D-exchange and TMT-based structural mapping. FDD discovered novel subunit-specific PTM signatures, including unusual nontop-surface N-glycosylations, that may drive subunit biases in human Cys-loop LGIC assembly and pharmacology, by redefining subunit/ligand interfaces and connecting function domains.
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Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, .,§Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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22
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Du YM, Xia T, Gu XQ, Wang T, Ma HY, Voglmeir J, Liu L. Rapid Sample Preparation Methodology for Plant N-Glycan Analysis Using Acid-Stable PNGase H+. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10550-5. [PMID: 26548339 DOI: 10.1021/acs.jafc.5b03633] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The quantification of potentially allergenic carbohydrate motifs of plant and insect glycoproteins is increasingly important in biotechnological and agricultural applications as a result of the use of insect cell-based expression systems and transgenic plants. The need to analyze N-glycan moieties in a highly parallel manner inspired us to develop a quick N-glycan analysis method based on a recently discovered bacterial protein N-glycanase (PNGase H(+)). In contrast to the traditionally used PNGase A, which is isolated from almond seeds and only releases N-glycans from proteolytically derived glycopeptides, the herein implemented PNGase H(+) allows for the release of N-glycans directly from the glycoprotein samples. Because PNGase H(+) is highly active under acidic conditions, the consecutive fluorescence labeling step using 2-aminobenzamide (2AB) can be directly performed in the same mixture used for the enzymatic deglycosylation step. All sample handling and incubation steps can be performed in less than 4 h and are compatible with microwell-plate sampling, without the need for tedious centrifugation, precipitation, or sample-transfer steps. The versatility of this methodology was evaluated by analyzing glycoproteins derived from various plant sources using ultra-performance liquid chromatography (UPLC) analysis and further demonstrated through the activity analysis of four PNGase H(+) mutant variants.
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Affiliation(s)
- Ya M Du
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Tian Xia
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Xiao Q Gu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Hong Y Ma
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, and ‡Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, People's Republic of China
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23
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Huang J, Wan H, Yao Y, Li J, Cheng K, Mao J, Chen J, Wang Y, Qin H, Zhang W, Ye M, Zou H. Highly Efficient Release of Glycopeptides from Hydrazide Beads by Hydroxylamine Assisted PNGase F Deglycosylation for N-Glycoproteome Analysis. Anal Chem 2015; 87:10199-204. [DOI: 10.1021/acs.analchem.5b02669] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Junfeng Huang
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Hao Wan
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- Shanghai
Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yating Yao
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Jinan Li
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Jiawei Mao
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Jin Chen
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Yan Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
- University of Chinese Academy of Sciences, Beijing, China, 100049
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Weibing Zhang
- Shanghai
Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China, 116023
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24
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Effects of selective cleavage of high-mannose-type glycans of Maackia amurensis leukoagglutinin on sialic acid-binding activity. Biochim Biophys Acta Gen Subj 2015; 1850:1815-21. [DOI: 10.1016/j.bbagen.2015.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 11/20/2022]
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25
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Weng Y, Sui Z, Jiang H, Shan Y, Chen L, Zhang S, Zhang L, Zhang Y. Releasing N-glycan from peptide N-terminus by N-terminal succinylation assisted enzymatic deglycosylation. Sci Rep 2015; 5:9770. [PMID: 25902405 PMCID: PMC4405948 DOI: 10.1038/srep09770] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/18/2015] [Indexed: 01/13/2023] Open
Abstract
Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification.
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Affiliation(s)
- Yejing Weng
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lingfan Chen
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Zhang
- 1] Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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26
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Sun G, Yu X, Bao C, Wang L, Li M, Gan J, Qu D, Ma J, Chen L. Identification and characterization of a novel prokaryotic peptide: N-glycosidase from Elizabethkingia meningoseptica. J Biol Chem 2015; 290:7452-62. [PMID: 25614628 DOI: 10.1074/jbc.m114.605493] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. Since its discovery in 1984, PNGase F has remained as the sole prokaryotic PNGase. Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. In this study, the candidate protein was expressed in vitro and was subjected to biochemical and structural analyses. The results revealed that it possesses PNGase activity and has substrate specificity different from that of PNGase F. The crystal structure of the protein was determined at 1.9 Å resolution. Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. These structural and functional analyses indicated that the candidate protein is a novel prokaryotic N-glycosidase. The protein has been named PNGase F-II.
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Affiliation(s)
- Guiqin Sun
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiang Yu
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Celimuge Bao
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Wang
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Meng Li
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianhua Gan
- the Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China, and
| | - Di Qu
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jinbiao Ma
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,
| | - Li Chen
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China,
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27
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Lomino JV, Naegeli A, Orwenyo J, Amin MN, Aebi M, Wang LX. A two-step enzymatic glycosylation of polypeptides with complex N-glycans. Bioorg Med Chem 2013; 21:2262-2270. [PMID: 23477942 DOI: 10.1016/j.bmc.2013.02.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/02/2013] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
A chemoenyzmatic method for direct glycosylation of polypeptides is described. The method consists of two site-specific enzymatic glycosylation steps: introduction of a glucose moiety at the consensus N-glycosylation sequence (NXS/T) in a polypeptide by an N-glycosyltransferase (NGT) and attachment of a complex N-glycan to the glucose primer by an endoglycosidase (ENGase)-catalyzed transglycosylation. Our experiments demonstrated that a relatively small excess of the UDP-Glc (the donor substrate) was sufficient for an effective glucosylation of polypeptides by the NGT, and different high-mannose and complex type N-glycans could be readily transferred to the glucose moiety by ENGases to provide full-size glycopeptides. The usefulness of the chemoenzymatic method was exemplified by an efficient synthesis of a complex glycoform of polypeptide C34, a potent HIV inhibitor derived from HIV-1 gp41. A comparative study indicated that the Glc-peptide was equally efficient as the natural GlcNAc-peptide to serve as an acceptor in the transglycosylation with sugar oxazoline as the donor substrate. Interestingly, the Glc-Asn linked glycopeptide was completely resistant to PNGase F digestion, in contrast to the GlcNAc-Asn linked natural glycopeptide that is an excellent substrate for hydrolysis. In addition, the Glc-Asn linked glycopeptide showed at least 10-fold lower hydrolytic activity toward Endo-M than the natural GlcNAc-Asn linked glycopeptide. The chemoenzymatic glycosylation method described here provides an efficient way to introducing complex N-glycans into polypeptides, for gain of novel properties that could be valuable for drug discovery.
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Affiliation(s)
- Joseph V Lomino
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Andreas Naegeli
- Institute of Microbiology, Dept. of Biology, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
| | - Jared Orwenyo
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Mohammed N Amin
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Markus Aebi
- Institute of Microbiology, Dept. of Biology, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
| | - Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
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28
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Kim YC, Jahren N, Stone MD, Udeshi ND, Markowski TW, Witthuhn BA, Shabanowitz J, Hunt DF, Olszewski NE. Identification and origin of N-linked β-D-N-acetylglucosamine monosaccharide modifications on Arabidopsis proteins. PLANT PHYSIOLOGY 2013; 161:455-64. [PMID: 23144189 PMCID: PMC3532274 DOI: 10.1104/pp.112.208900] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/05/2012] [Indexed: 05/20/2023]
Abstract
Many plant proteins are modified with N-linked oligosaccharides at asparagine-X-serine/threonine sites during transit through the endoplasmic reticulum and the Golgi. We have identified a number of Arabidopsis (Arabidopsis thaliana) proteins with modifications consisting of an N-linked N-acetyl-D-glucosamine monosaccharide (N-GlcNAc). Electron transfer dissociation mass spectrometry analysis of peptides bearing this modification mapped the modification to asparagine-X-serine/threonine sites on proteins that are predicted to transit through the endoplasmic reticulum and Golgi. A mass labeling method was developed and used to study N-GlcNAc modification of two thioglucoside glucohydrolases (myrosinases), TGG1 and TGG2 (for thioglucoside glucohydrolase). These myrosinases are also modified with high-mannose (Man)-type glycans. We found that N-GlcNAc and high-Man-type glycans can occur at the same site. It has been hypothesized that N-GlcNAc modifications are generated when endo-β-N-acetylglucosaminidase (ENGase) cleaves N-linked glycans. We examined the effects of mutations affecting the two known Arabidopsis ENGases on N-GlcNAc modification of myrosinase and found that modification of TGG2 was greatly reduced in one of the single mutants and absent in the double mutant. Surprisingly, N-GlcNAc modification of TGG1 was not affected in any of the mutants. These data support the hypothesis that ENGases hydrolyze high-Man glycans to produce some of the N-GlcNAc modifications but also suggest that some N-GlcNAc modifications are generated by another mechanism. Since N-GlcNAc modification was detected at only one site on each myrosinase, the production of the N-GlcNAc modification may be regulated.
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29
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Fallah MA, Huck V, Niemeyer V, Desch A, Angerer JI, McKinnon TAJ, Wixforth A, Schneider SW, Schneider MF. Circulating but not immobilized N-deglycosylated von Willebrand factor increases platelet adhesion under flow conditions. BIOMICROFLUIDICS 2013; 7:44124. [PMID: 24404057 PMCID: PMC3772935 DOI: 10.1063/1.4819746] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 08/13/2013] [Indexed: 05/10/2023]
Abstract
The role of von Willebrand factor (VWF) as a shear stress activated platelet adhesive has been related to a coiled-elongated shape conformation. The forces dominating this transition have been suggested to be controlled by the proteins polymeric architecture. However, the fact that 20% of VWF molecular weight originates from glycan moieties has so far been neglected in these calculations. In this study, we present a systematic experimental investigation on the role of N-glycosylation for VWF mediated platelet adhesion under flow. A microfluidic flow chamber with a stenotic compartment that allows one to mimic various physiological flow conditions was designed for the efficient analysis of the adhesion spectrum. Surprisingly, we found an increase in platelet adhesion with elevated shear rate, both qualitatively and quantitatively fully conserved when N-deglycosylated VWF (N-deg-VWF) instead of VWF was immobilized in the microfluidic channel. This has been demonstrated consistently over four orders of magnitude in shear rate. In contrast, when N-deg-VWF was added to the supernatant, an increase in adhesion rate by a factor of two was detected compared to the addition of wild-type VWF. It appears that once immobilized, the role of glycans is at least modified if not-as found here for the case of adhesion-negated. These findings strengthen the physical impact of the circulating polymer on shear dependent platelet adhesion events. At present, there is no theoretical explanation for an increase in platelet adhesion to VWF in the absence of its N-glycans. However, our data indicate that the effective solubility of the protein and hence its shape or conformation may be altered by the degree of glycosylation and is therefore a good candidate for modifying the forces required to uncoil this biopolymer.
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Affiliation(s)
- M A Fallah
- University of Augsburg, Chair of Experimental Physics I, 86159 Augsburg, Germany ; Department of Biophysical Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - V Huck
- Heidelberg University, Medical Faculty Mannheim, Experimental Dermatology, 68167 Mannheim, Germany
| | - V Niemeyer
- Heidelberg University, Medical Faculty Mannheim, Experimental Dermatology, 68167 Mannheim, Germany
| | - A Desch
- Heidelberg University, Medical Faculty Mannheim, Experimental Dermatology, 68167 Mannheim, Germany
| | - J I Angerer
- University of Augsburg, Chair of Experimental Physics I, 86159 Augsburg, Germany
| | - T A J McKinnon
- Imperial College London, Hammersmith Hospital Campus, Department of Medicine, London W12 0NN, United Kingdom
| | - A Wixforth
- University of Augsburg, Chair of Experimental Physics I, 86159 Augsburg, Germany
| | - S W Schneider
- Heidelberg University, Medical Faculty Mannheim, Experimental Dermatology, 68167 Mannheim, Germany
| | - M F Schneider
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, USA
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30
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Neville DC, Alonzi DS, Butters TD. Hydrophilic interaction liquid chromatography of anthranilic acid-labelled oligosaccharides with a 4-aminobenzoic acid ethyl ester-labelled dextran hydrolysate internal standard. J Chromatogr A 2012; 1233:66-70. [DOI: 10.1016/j.chroma.2012.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/24/2012] [Accepted: 02/01/2012] [Indexed: 11/25/2022]
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31
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Gerlach JQ, Kilcoyne M, Farrell MP, Kane M, Joshi L. Differential release of high mannose structural isoforms by fungal and bacterial endo-β-N-acetylglucosaminidases. MOLECULAR BIOSYSTEMS 2012; 8:1472-81. [DOI: 10.1039/c2mb05455h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Babiuch K, Becer CR, Gottschaldt M, Delaney JT, Weisser J, Beer B, Wyrwa R, Schnabelrauch M, Schubert US. Adhesion of Preosteoblasts and Fibroblasts onto Poly(pentafluorostyrene)-Based Glycopolymeric Films and their Biocompatibility. Macromol Biosci 2011; 11:535-48. [DOI: 10.1002/mabi.201000374] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/16/2010] [Indexed: 12/15/2022]
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33
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Valliere-Douglass JF, Eakin CM, Wallace A, Ketchem RR, Wang W, Treuheit MJ, Balland A. Glutamine-linked and non-consensus asparagine-linked oligosaccharides present in human recombinant antibodies define novel protein glycosylation motifs. J Biol Chem 2010; 285:16012-22. [PMID: 20233717 DOI: 10.1074/jbc.m109.096412] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the presence of oligosaccharide structures on a glutamine residue present in the V(L) domain sequence of a recombinant human IgG2 molecule. Residue Gln-106, present in the QGT sequence following the rule of an asparagine-linked consensus motif, was modified with biantennary fucosylated oligosaccharide structures. In addition to the glycosylated glutamine, analysis of a lectin-enriched antibody population showed that 4 asparagine residues: heavy chain Asn-162, Asn-360, and light chain Asn-164, both of which are present in the IgG1 and IgG2 constant domain sequences, and Asn-35, which was present in CDR(L)1, were also modified with oligosaccharide structures at low levels. The primary sequences around these modified residues do not adhere to the N-linked consensus sequon, NX(S/T). Modeling of these residues from known antibody crystal structures and sequence homology comparison indicates that non-consensus glycosylation occurs on Asn residues in the context of a reverse consensus motif (S/T)XN located on highly flexile turns within 3 residues of a conformational change. Taken together our results indicate that protein glycosylation is governed by more diversified requirements than previously appreciated.
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34
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Huang W, Groothuys S, Heredia A, Kuijpers BHM, Rutjes FPJT, van Delft FL, Wang LX. Enzymatic glycosylation of triazole-linked GlcNAc/Glc-peptides: synthesis, stability and anti-HIV activity of triazole-linked HIV-1 gp41 glycopeptide C34 analogues. Chembiochem 2009; 10:1234-42. [PMID: 19353609 DOI: 10.1002/cbic.200800741] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Long-lasting sweet proteins: The chemoenzymatic synthesis of a triazole (T)-linked glycosylated C34 fragment from HIV-1 gp41 is described. The glycopeptide shows high solubility, excellent fusion inhibition, and as shown in the graph, promising protease resistance. Endoglycosidase-catalyzed transglycosylation of triazole-linked glucose (Glc) and N-acetylglucosamine (GlcNAc)-containing dipeptides and polypeptides was achieved by using synthetic sugar oxazoline as the donor substrate. It was found that both N- and C-linked Glc/GlcNAc-containing triazole derivatives were effective substrates for endo-beta-N-acetylglucosaminidase from Arthrobacter (Endo-A) for transglycosylation; this demonstrates a broad acceptor substrate specificity for Endo-A. This chemoenzymatic method was successfully used for the synthesis of a novel triazole-linked C34 glycopeptide derived from the HIV-1 envelope glycoprotein, gp41. We found that the synthetic C34 glycopeptide possesses potent anti-HIV activity with an IC(50) of 21 nM. The triazole-linked C34 glycopeptide demonstrated a much enhanced stability against protease- and glycoamidase-catalyzed digestion; this shows the protective effects of glycosylation and the stability of the triazole linkage. These favorable properties suggest that the triazole-linked C34 glycopeptide might be valuable for further development as an anti-HIV drug candidate.
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Affiliation(s)
- Wei Huang
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
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35
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Neville DCA, Dwek RA, Butters TD. Development of a single column method for the separation of lipid- and protein-derived oligosaccharides. J Proteome Res 2009; 8:681-7. [PMID: 19099509 DOI: 10.1021/pr800704t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent labeling of oligosaccharides with anthranilic acid (2-aminobenzoic acid; 2AA), or 2-aminobenzamide (2AB) permits the rapid, sensitive analysis of structures present in cells and tissues. Normal-phase (NP)/hydrophilic interaction chromatography (HILIC) is commonly used to separate fluorophore-derivatized oligosaccharides. Column elution is expressed as glucose units (GU) following calculation of relative retention when compared to an external glucose oligomer standard. However, there is significant overlap between sialylated and neutral oligosaccharides. Normal-phase anion-exchange (NP-AE) HPLC can separate differing classes of oligosaccharides according to the number of charged residues, but relative retention times in GU cannot be calculated across the entire gradient. We have overcome this difficulty by use of a Dionex AS11 column that combines both hydrophilic interaction and anion-exchange chromatographies, termed HIAX, which enables the calculation of GU values for oligosaccharides that carry sialylated or other negatively charged groups. The same method may also be employed for 2AB and other fluorophore-labeled oligosaccharides. Additionally, the same HPLC eluants are used for the differing HPLC columns. Therefore, analysis of HILIC- or HIAX-separated fluorophore-labeled oligosaccharides can be performed using a single HPLC system with a single set of eluents following a simple column change.
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Affiliation(s)
- David C A Neville
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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36
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Abstract
Molecular imaging enables visualization of specific molecules in vivo and without substantial perturbation to the target molecule's environment. Glycans are appealing targets for molecular imaging but are inaccessible with conventional approaches. Classic methods for monitoring glycans rely on molecular recognition with probe-bearing lectins or antibodies, but these techniques are not well suited to in vivo imaging. In an emerging strategy, glycans are imaged by metabolic labeling with chemical reporters and subsequent ligation to fluorescent probes. This technique has enabled visualization of glycans in living cells and in live organisms such as zebrafish. Molecular imaging with chemical reporters offers a new avenue for probing changes in the glycome that accompany development and disease.
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37
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Nuck R. Enzymatical hydrolysis of N-glycans from glycoproteins and fluorescent labeling by 2-aminobenzamide (2-AB). Methods Mol Biol 2008; 446:231-238. [PMID: 18373261 DOI: 10.1007/978-1-60327-084-7_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
When performing a structural analysis of N-glycans, a number of aspects should be considered. N-Glycans may be hydrolyzed from purifi ed glyc-oproteins, serum glycoprotein mixtures, or delipidated membrane fractions by chemical hydrolysis using hydrazine or enzymatic hydrolysis using PNGase F. Chemical deglycosylation may be an economical alternative to produce N-and O-glycans in a preparative scale, but it is less suitable for analytical purposes. By chemical hydrazinolysis the protein core is destroyed completely and all acyl groups are cleaved from neuraminic acid residues as well as from N-acetylhexosamine residues. If not only a structure analysis of N-glycans is intended but a sequencing of the protein core, an analysis of the different types of neuraminic acids or an elucidation of the carbohydrate structures in distinct glycosylation sites has to be performed in addition, enzymatical deglycosylation using PNGase F is the most suitable way to hydrolyze N-glycans from the protein backbone.
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Affiliation(s)
- Rolf Nuck
- Institut für Molekularbiologie und Biochemie, Charité - Universitaetsmedizin Berlin, Berlin-Dahlem, Germany
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38
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Suzuki T, Hara I, Nakano M, Zhao G, Lennarz WJ, Schindelin H, Taniguchi N, Totani K, Matsuo I, Ito Y. Site-specific Labeling of Cytoplasmic Peptide:N-Glycanase by N,N′-Diacetylchitobiose-related Compounds. J Biol Chem 2006; 281:22152-22160. [PMID: 16740630 DOI: 10.1074/jbc.m603236200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide:N-glycanase (PNGase) is the deglycosylating enzyme, which releases N-linked glycan chains from N-linked glycopeptides and glycoproteins. Recent studies have revealed that the cytoplasmic PNGase is involved in the degradation of misfolded/unassembled glycoproteins. This enzyme has a Cys, His, and Asp catalytic triad, which is required for its enzymatic activity and can be inhibited by "free" N-linked glycans. These observations prompted us to investigate the possible use of haloacetamidyl derivatives of N-glycans as potent inhibitors and labeling reagents of this enzyme. Using a cytoplasmic PNGase from budding yeast (Png1), Man9GlcNAc2-iodoacetoamide was shown to be a strong inhibitor of this enzyme. The inhibition was found to be through covalent binding of the carbohydrate to a single Cys residue on Png1, and the binding was highly selective. The mutant enzyme in which Cys191 of the catalytic triad was changed to Ala did not bind to the carbohydrate probe, suggesting that the catalytic Cys is the binding site for this compound. Precise determination of the carbohydrate attachment site by mass spectrometry clearly identified Cys191 as the site of covalent attachment. Molecular modeling of N,N'-diacetylchitobiose (chitobiose) binding to the protein suggests that the carbohydrate binding site is distinct from but adjacent to that of Z-VAD-fmk, a peptide-based inhibitor of this enzyme. These results suggest that cytoplasmic PNGase has a separate binding site for chitobiose and other carbohydrates, and haloacetamide derivatives can irreversibly inhibit that catalytic Cys in a highly specific manner.
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Affiliation(s)
- Tadashi Suzuki
- 21st Center of Excellence Program, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.
| | - Izumi Hara
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Miyako Nakano
- 21st Center of Excellence Program, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Gang Zhao
- Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215
| | - William J Lennarz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215
| | - Hermann Schindelin
- Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215; Rudolf Virchow Center for Experimental Biomedicine and Institute of Structural Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Naoyuki Taniguchi
- 21st Center of Excellence Program, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan; Department of Disease Glycomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kiichiro Totani
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan; RIKEN, The Institute of Physical and Chemical Research, Wako 351-0198, Japan
| | - Ichiro Matsuo
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan; RIKEN, The Institute of Physical and Chemical Research, Wako 351-0198, Japan
| | - Yukishige Ito
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan; RIKEN, The Institute of Physical and Chemical Research, Wako 351-0198, Japan
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39
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Disney MD, Hook DF, Namoto K, Seeberger PH, Seebach D. N-Linked Glycosylatedβ-Peptides Are Resistant to Degradation by Glycoamidase A. Chem Biodivers 2005; 2:1624-34. [PMID: 17191959 DOI: 10.1002/cbdv.200590132] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Beta-peptides are resistant to degradation by a variety of proteolytic enzymes that rapidly degrade natural alpha-peptides. This is one of many characteristics that make beta-peptides an attractive class of compounds for drug discovery efforts. To further understand the molecular recognition properties of beta-peptides and the ability of enzymes to degrade them, we have synthesized a series of N-linked glycosylated beta- and alpha-peptides, and tested their stability towards a glycosidase. We found that glyco-beta-peptides that contain N-acetylglucosamine (1) or N,N-diacetylchitobiose (2) are completely stable to degradation by glycoamidase A. In comparison, the glyco-alpha-peptides 3 and 4 containing N-acetylglucosamine or N,N-diacetylchitobiose are degraded. Inhibition experiments using increasing concentrations of a glyco-beta-peptide fail to inhibit degradation of the corresponding glyco-alpha-peptide, even when the glyco-beta-peptide is at a 128-fold higher concentration than the glyco-alpha-peptide. Evidently, the glyco-beta-peptides have a much weaker affinity for the active site of the glycosidase than the corresponding glyco-alpha-peptide. These and the results with proteolytic enzymes suggest that the additional CH(2) group introduced into the alpha-amino acid residues causes beta-peptides not to be recognized by hydrolytic enzymes. The results described herein suggest the potential of beta-peptides that are functionalized with carbohydrates for biological and biomedical investigations, without having to be concerned about the carbohydrate being removed.
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Affiliation(s)
- Matthew D Disney
- Laboratorium für Organische Chemie, Department für Chemie und Angewandte Biowissenschaften, Eidgenössische Technische Hochschule Zürich, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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40
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Li JS, Cui L, Rock DL, Li J. Novel glycosidic linkage in Aedes aegypti chorion peroxidase: N-mannosyl tryptophan. J Biol Chem 2005; 280:38513-21. [PMID: 16150691 DOI: 10.1074/jbc.m508449200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aedes aegypti chorion peroxidase (CPO) plays a crucial role in chorion hardening by catalyzing chorion protein cross-linking through dityrosine formation. The enzyme is extremely resistant to denaturing conditions, which seem intimately related to its post-translational modifications, including disulfide bond formation and glycosylation. In this report, we have provided data that describe a new type of glycosylation in CPO, where a mannose is linked to the N-1 atom of the indole ring of Trp residue. Through liquid chromatography/electrospray ionization/tandem mass spectrometry and de novo sequencing of CPO tryptic peptides, we determined that three of the seven available Trp residues in mature CPO are partially (40-50%) or completely mannosylated. This conclusion is based on the following properties of the electrospray ionization/tandem mass spectrometry spectra and the enzymatic reaction of these peptides: 1) the presence of a 162-Da substituent in each Trp residue; 2) the presence of abundant fragments of m/z 163 ([Hex + H]) and [M + H - 162] (typical for N-glycosides); 3) the absence of a loss of 120 Da (this loss is typical for aromatic C-glycosides); and 4) the cleavage of the glycosidic linkage by PNGase A or F (typical for N-glycans). These results establish that a C-N bond is formed between the anomeric carbon of a mannose residue and the N-1 atom of the indole ring of Trp. This is the first report that provides definitive evidence for N-mannosylation of Trp residues in a protein. In addition, our data demonstrate that PNGase can hydrolyze Trp N-linked mannose in peptides, which is unusual because no typical beta-amide bond is present in the Trp-mannosyl moiety. Results of this study should stimulate research toward a comprehensive understanding of physiology and biochemistry of Trp N-mannosylation in proteins and the overall biochemical mechanisms of PNGase-catalyzed reactions.
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Affiliation(s)
- Junsuo S Li
- Department of Pathobiology, University of Illinois, Urbana, Illinois 61802, USA
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Isordia-Salas I, Pixley RA, Parekh H, Kunapuli SP, Li F, Stadnicki A, Lin Y, Sartor RB, Colman RW. The mutation Ser511Asn leads to N-glycosylation and increases the cleavage of high molecular weight kininogen in rats genetically susceptible to inflammation. Blood 2003; 102:2835-42. [PMID: 12842992 DOI: 10.1182/blood-2003-02-0661] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Crohn disease is immunologically mediated and characterized by intestinal and systemic chronic inflammation. In a rat model, injection of peptidoglycan-polysaccharide complexes into the intestinal wall induced chronic inflammation in Lewis but neither Fischer nor Buffalo rats, indicating a differential genetic susceptibility. Proteolysis of plasma high molecular weight kininogen (HK) yielding bradykinin and cleaved HK (HKa) was faster in Lewis than in Fischer or Buffalo rat plasma. A single point mutation at nucleotide 1586 was found translating from Ser511 (Buffalo and Fisher) to Asn511 (Lewis). The latter defines an Asn-Xaa-Thr consensus sequence for N-glycosylation. We expressed these domains in Escherichia coli and found no differences in the rate of cleavage by purified kallikrein in the 3 strains in the absence of N-glycosylation. We then expressed these domains in Chinese hamster ovary (CHO) cells, which are capable of glycosylation, and found an increased rate of cleavage of Lewis HK. The Lewis mutation is associated with N-glycosylation as evidenced by a more rapid migration after treatment with N-glycosidase F. When CHO cells were cultured in the presence of tunicamycin, the kallikrein-induced cleavage rate of Lewis HK was not increased. This molecular alteration might be one contributing factor resulting in chronic inflammation in Lewis rats.
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Affiliation(s)
- Irma Isordia-Salas
- The Sol Sherry Thrombosis Research Center, Temple University School of Medicine, 3400 North Broad St, Philadelphia, PA 19140, USA
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42
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Choi O, Tomiya N, Kim JH, Slavicek JM, Betenbaugh MJ, Lee YC. N-glycan structures of human transferrin produced by Lymantria dispar (gypsy moth) cells using the LdMNPV expression system. Glycobiology 2003; 13:539-48. [PMID: 12672704 DOI: 10.1093/glycob/cwg071] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
N-glycan structures of recombinant human serum transferrin (hTf) expressed by Lymantria dispar (gypsy moth) 652Y cells were determined. The gene encoding hTf was incorporated into a Lymantria dispar nucleopolyhedrovirus (LdMNPV) under the control of the polyhedrin promoter. This virus was then used to infect Ld652Y cells, and the recombinant protein was harvested at 120 h postinfection. N-glycans were released from the purified recombinant human serum transferrin and derivatized with 2-aminopyridine; the glycan structures were analyzed by a two-dimensional HPLC and MALDI-TOF MS. Structures of 11 glycans (88.8% of total N-glycans) were elucidated. The glycan analysis revealed that the most abundant glycans were Man1-3(+/-Fucalpha6)GlcNAc2 (75.5%) and GlcNAcMan3(+/-Fucalpha6)GlcNAc2 (7.4%). There was only approximately 6% of high-mannose type glycans identified. Nearly half (49.8%) of the total N-glycans contained alpha(1,6)-fucosylation on the Asn-linked GlcNAc residue. However alpha(1,3)-fucosylation on the same GlcNAc, often found in N-glycans produced by other insects and insect cells, was not detected. Inclusion of fetal bovine serum in culture media had little effect on the N-glycan structures of the recombinant human serum transferrin obtained.
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Affiliation(s)
- One Choi
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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Affiliation(s)
- Y C Lee
- Biology Department, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA.
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Haneda K, Inazu T, Mizuno M, Iguchi R, Tanabe H, Fujimori K, Yamamoto K, Kumagai H, Tsumori K, Munekata E. Chemo-enzymatic synthesis of a bioactive peptide containing a glutamine-linked oligosaccharide and its characterization. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1526:242-8. [PMID: 11410333 DOI: 10.1016/s0304-4165(01)00135-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A bioactive peptide containing a glutamine-linked oligosaccharide was chemo-enzymatically synthesized by use of the solid-phase method of peptide synthesis and the transglycosylation activity of endo-beta-N-acetylglucosaminidase. Substance P, a neuropeptide, is an undecapeptide containing two L-glutamine residues. A substance P derivative with an N-acetyl-D-glucosamine residue attached to the fifth or sixth L-glutamine residue from the N-terminal region was chemically synthesized. A sialo complex-type oligosaccharide derived from a glycopeptide of hen egg yolk was added to the N-acetyl-D-glucosamine moiety of the substance P derivative using the transglycosylation activity of endo-beta-N-acetylglucosaminidase from Mucor hiemalis, and a substance P derivative with a sialo complex-type oligosaccharide attached to the L-glutamine residue was synthesized. This glycosylated substance P was biologically active, although the activity was rather low, and stable against peptidase digestion. The oligosaccharide moiety attached to the L-glutamine residue of the peptide was not liberated by peptide-N(4)-(N-acetyl-beta-D-glucosaminyl) asparagine amidase F.
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Affiliation(s)
- K Haneda
- The Noguchi Institute, Itabashi, Tokyo, Japan.
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Fujita K, Takegawa K. Chemoenzymatic synthesis of neoglycoproteins using transglycosylation with endo-beta-N-acetylglucosaminidase A. Biochem Biophys Res Commun 2001; 282:678-82. [PMID: 11401514 DOI: 10.1006/bbrc.2001.4631] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel chemoenzymatic approach to synthesize neoglycoproteins containing high-mannose-type oligosaccharides is described. p-Isothiocyanatophenyl-beta-d-glucopyranoside (Glc-ITC) was transferred to the reducing end of the high-mannose-type oligosaccharides using a transglycosylation activity of endo-beta-N-acetylglucosaminidase A (Endo-A). A novel oligosaccharide, Man(6)GlcNAc-Glc-ITC, was synthesized as a coupling reagent for lysyl and N-terminal residues of the protein moiety. The neoglycoconjugate was coupled with several nonglycosylated proteins such as ribonuclease A, lysozyme, and alpha-lactalbumin. Between one and four high-mannose-type oligosaccharides were incorporated per molecule of these proteins. This method should be very useful for the synthesis of neoglycoproteins with homogeneous high-mannose-type oligosaccharides.
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Affiliation(s)
- K Fujita
- Department of Life Sciences, Kagawa University, Miki-cho, Kagawa, 761-0795, Japan
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Abstract
Despite the omnipresence of protein glycosylation in nature, little is known about how the attachment of carbohydrates affects peptide and protein activity. One reason is the lack of a straightforward method to access biologically relevant glycopeptides and glycoproteins. The isolation of homogeneous glycopeptides from natural sources is complicated by the heterogeneity of naturally occuring glycoproteins. It is chemical and chemoenzymatic synthesis that is meeting the challenge to solve this availability problem, thus playing a key role for the advancement of glycobiology. The current art of glycopeptide synthesis, albeit far from being routine, has reached a level of maturity that allows for the access to homogeneous and pure material for biological and medicinal research. Even the ambitious goal of the total synthesis of an entire glycoprotein is within reach. It is demonstrated that with the help of synthetic glycopeptides the effects of glycosylation on protein structure and function can be studied in molecular detail. For example, in immunology, synthetic (tumour-specific) glycopeptides can be used as immunogens to elicit a tumour-cell-specific immune response. Again, synthetic glycopeptides are an invaluable tool to determine the fine specificity of the immune response that can be mediated by both carbohydrate-specific B and T cells. Furthermore, selected examples for the use of synthetic glycopeptides as ligands of carbohydrate-binding proteins and as enzyme substrates or inhibitors are presented.
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Affiliation(s)
- O Seitz
- Department of Chemical Biology Max-Planck-Institut für molekulare Physiologie Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Ohki R, Nemoto J, Murasawa H, Oda E, Inazawa J, Tanaka N, Taniguchi T. Reprimo, a new candidate mediator of the p53-mediated cell cycle arrest at the G2 phase. J Biol Chem 2000; 275:22627-30. [PMID: 10930422 DOI: 10.1074/jbc.c000235200] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A novel gene, Reprimo, in which induction in cells exposed to X-irradiation is dependent on p53 expression, has been isolated. Ectopic p53 expression results in the induction of its mRNA. Reprimo is a highly glycosylated protein and, when ectopically expressed, it is localized in the cytoplasm and induces G(2) arrest of the cell cycle. In the arrested cells, both Cdc2 activity and nuclear translocation of cyclin B1 are inhibited, suggesting the involvement of Reprimo in the Cdc2.cyclin B1 regulation pathway. Thus, Reprimo may be a new member involved in the regulation of p53-dependent G(2) arrest of the cell cycle.
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Affiliation(s)
- R Ohki
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Deras IL, Sano M, Kato I, Lee YC. Assay of glycoamidases and endo-beta-N-acetylglucosaminidases by lectin capture and dissociation-enhanced lanthanide fluorescence immunoassay. Anal Biochem 2000; 278:213-20. [PMID: 10660465 DOI: 10.1006/abio.1999.4458] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed an assay system for endo-beta-N-acetylglucosaminidase and glycoamidase (PNGase), using Eu(3+)-labeled Man(9)GlcNAc(2) glycopeptides as substrates in combination with lectin capture. Two glycopeptides of different peptide lengths, derived from soybean agglutinin, were labeled with Eu(3+) via a diethylenetriaminepentaacetate (DTPA) chelating linker and served as substrates for two types of enzymes: one with (Man(9)GlcNAc(2))Asn for endo-beta-N-acetylglucosaminidase and the other with Ala-Ser-Phe-(Man(9)GlcNAc(2))Asn-Phe-Thr for glycoamidase activities. Following enzymatic hydrolysis, concanavalin A, immobilized or soluble, was added to the mixture to bind unreacted substrate and unlabeled hydrolysis product. The labeled peptide product could then be separated from the lectin-bound complexes by filtration for quantification by dissociation-enhanced lanthanide fluorescence immunoassay. Activities as low as 2 fmol min(-1) could be rapidly quantified for both types of enzymes, and enzymological parameters could be determined within minutes. Applicability of the assay was tested for identification of a glycoamidase activity peak in the fractionation of sweet almond emulsin, a classic example. This assay offers sensitivity, ease of use, and high throughput. In addition, it is versatile and should be applicable to other glycobiology enzyme systems.
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Affiliation(s)
- I L Deras
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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A strategy for the identification of site-specific glycosylation in glycoproteins using MALDI TOF MS. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0957-4166(99)00545-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Svetek J, Yadav MP, Nothnagel EA. Presence of a glycosylphosphatidylinositol lipid anchor on rose arabinogalactan proteins. J Biol Chem 1999; 274:14724-33. [PMID: 10329668 DOI: 10.1074/jbc.274.21.14724] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arabinogalactan proteins constitute a class of plant cell surface proteoglycans with widespread occurrence and suggested functions in various aspects of plant growth and development, including cell proliferation, expansion, marking, and death. Previous investigations of subcellular fractions from suspension-cultured cells of "Paul's Scarlet" rose (Rosa sp.) have revealed extensive structural similarity between some soluble arabinogalactan proteins from the cell wall space and some plasma membrane-associated arabinogalactan proteins, thus inspiring the present investigation of the mechanism through which these inherently water-soluble molecules are held on the plasma membrane. Several lines of evidence gained through a combination of methods including reversed-phase chromatography, treatment with phosphatidylinositol-specific phospholipase C, and chemical structural analysis now show that some rose arabinogalactan proteins carry a ceramide class glycosylphosphatidylinositol lipid anchor. The predominant form of the ceramide is composed of tetracosanoic acid and 4-hydroxysphinganine. Plasma membrane vesicles readily shed arabinogalactan proteins by an inherent mechanism that appears to involve a phospholipase. This finding has significance toward understanding the biosynthesis, localization, and function of arabinogalactan proteins and toward stimulating other studies that may expand the currently very short list of higher plant proteins found to carry such membrane lipid anchors.
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Affiliation(s)
- J Svetek
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124, USA
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