1
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Heindel DW, Figueroa Acosta DM, Goff M, Yengo CK, Jan M, Liu X, Wang XH, Petrova MI, Zhang M, Sagar M, Barnette P, Pandey S, Hessell AJ, Chan KW, Kong XP, Chen BK, Mahal LK, Bensing BA, Hioe CE. HIV-1 interaction with an O-glycan-specific bacterial lectin enhances virus infectivity and resistance to neutralization by antibodies. RESEARCH SQUARE 2024:rs.3.rs-2596269. [PMID: 36824869 PMCID: PMC9949255 DOI: 10.21203/rs.3.rs-2596269/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bacteria dysbiosis has been associated with an increased risk of HIV-1 transmission and acquisition. The prevalent idea is that bacteria dysbiosis compromises mucosal integrity and promotes inflammatory conditions to cause recruitment and activation of immune cells that harbor or are targeted by HIV-1. However, it is also possible that HIV-1 directly binds bacteria or bacterial products to impact virus infectivity and transmissibility. This study evaluated HIV-1 interactions with bacteria through glycan-binding lectins. The Streptococcal Siglec-like lectin SLBR-N, which is part of the fimbriae shrouding the bacteria surface and recognizes α2,3 sialyated O-linked glycans, was noted for its ability to enhance HIV-1 infectivity in the context of cell-free infection and cell-to-cell transfer. Enhancing effects were recapitulated with O-glycan-binding plant lectins, signifying the importance of O-glycans. Conversely, N-glycan-binding bacterial lectins FimH and Msl had no effect. SLBR-N was demonstrated to capture and transfer infectious HIV-1 virions, bind to O-glycans on HIV-1 Env, and increase HIV-1 resistance to broadly neutralizing antibodies targeting different regions of Env. Hence, this study highlights the potential contribution of O-glycans in promoting HIV-1 infection through the exploitation of O-glycan-binding lectins from commensal bacteria at the mucosa.
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Affiliation(s)
- Daniel W Heindel
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dania M Figueroa Acosta
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marisa Goff
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clauvis Kunkeng Yengo
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Muzafar Jan
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Present address: Department of Biochemistry, Government Degree College Handwara, University of Kashmir, Jammu & Kashmir, India
| | - Xiaomei Liu
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiao-Hong Wang
- VA New York Harbor Healthcare System-Manhattan, New York, New York, United States of America
| | - Mariya I Petrova
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Present address: Microbiome Insights and Probiotics Consultancy, Karlovo, Bulgaria
| | - Mo Zhang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Manish Sagar
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Phillip Barnette
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Shilpi Pandey
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology New York University Grossman School of Medicine, New York, NY, USA
| | - Benjamin K Chen
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Barbara A Bensing
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, CA, USA
| | - Catarina E Hioe
- Divison of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, USA
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2
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Glycosylation of ALV-J envelope protein at sites 17 and 193 is pivotal in the virus replication. J Virol 2021; 96:e0154921. [PMID: 34878920 PMCID: PMC8865534 DOI: 10.1128/jvi.01549-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycans on envelope glycoprotein (Env) of the subgroup J avian leukosis virus (ALV-J) play an essential role in virion integrity and infection process. In this study, we found that among the 13 predicted N-linked glycosylation sites (NGSs) in gp85 of Tibetan chicken strain TBC-J6, N17 and N193/N191 are pivotal in the virus replication. Further research illustrated that mutation at N193 weakened Env-receptor binding in blocking assay of viral entrance, co-immunoprecipitation and ELISA. Our studies also showed that N17 was involved in Env protein processing and later virion incorporation, based on the detection of p27 and Env protein in the supernatant and gp37 in the cell culture. This report is a systematic research on clarifying the biological function of NGSs on ALV-J gp85, which would provide valuable insights in the role of gp85 in ALV life cycle as well as anti-ALV-J strategies. Importance ALV-J is a retrovirus that can cause multiple types of tumors in chickens. Among all the viral proteins, the heavily glycosylated envelope protein is especially crucial. Glycosylation plays a major role in Env protein function, including protein processing, receptor attachment and immune evasion. Notably, viruses isolated recently seem to lose the 6th and 11st NGSs, which are proved to be important in receptor binding. In our study, the 1st (N17) and 8th (N193) NGS of gp85 of strain TBC-J6 can largely influence the titer of this virus. Deglycosylation at N193 weakened Env-receptor binding, while mutation at N17 influenced Env protein processing. This study systemically analyzed the function of NGSs in ALV-J in different aspects, which may help us to understand the lifecycle of ALV-J and provide antiviral targets for the control of ALV-J.
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3
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Zhang Y, Zheng S, Zhao W, Mao Y, Cao W, Zeng W, Liu Y, Hu L, Gong M, Cheng J, Chen Y, Yang H. Sequential Analysis of the N/O-Glycosylation of Heavily Glycosylated HIV-1 gp120 Using EThcD-sceHCD-MS/MS. Front Immunol 2021; 12:755568. [PMID: 34745128 PMCID: PMC8567067 DOI: 10.3389/fimmu.2021.755568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/06/2021] [Indexed: 02/05/2023] Open
Abstract
Deciphering the glycosylation of the viral envelope (Env) glycoprotein is critical for evaluating viral escape from the host’s immune response and developing vaccines and antiviral drugs. However, it is still challenging to precisely decode the site-specific glycosylation characteristics of the highly glycosylated Env proteins, although glycoproteomics have made significant advances in mass spectrometry techniques and data analysis tools. Here, we present a hybrid dissociation technique, EThcD-sceHCD, by combining electron transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) into a sequential glycoproteomic workflow. Following this scheme, we characterized site-specific N/O-glycosylation of the human immunodeficiency virus type 1 (HIV-1) Env protein gp120. The EThcD-sceHCD method increased the number of identified glycopeptides when compared with EThcD, while producing more comprehensive fragment ions than sceHCD for site-specific glycosylation analysis, especially for accurate O-glycosite assignment. Finally, eighteen N-glycosites and five O-glycosites with attached glycans were assigned unambiguously from heavily glycosylated gp120. These results indicate that our workflow can achieve improved performance for analysis of the N/O-glycosylation of a highly glycosylated protein containing numerous potential glycosites in one process. Knowledge of the glycosylation landscape of the Env glycoprotein will be useful for understanding of HIV-1 infection and development of vaccines and drugs.
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Affiliation(s)
- Yong Zhang
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Cao
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wenjuan Zeng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yueqiu Liu
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Younan Chen
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
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4
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Stevenson-Leggett P, Armstrong S, Keep S, Britton P, Bickerton E. Analysis of the avian coronavirus spike protein reveals heterogeneity in the glycans present. J Gen Virol 2021; 102. [PMID: 34424155 PMCID: PMC8513636 DOI: 10.1099/jgv.0.001642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an economically important coronavirus, causing damaging losses to the poultry industry worldwide as the causative agent of infectious bronchitis. The coronavirus spike (S) glycoprotein is a large type I membrane protein protruding from the surface of the virion, which facilitates attachment and entry into host cells. The IBV S protein is cleaved into two subunits, S1 and S2, the latter of which has been identified as a determinant of cellular tropism. Recent studies expressing coronavirus S proteins in mammalian and insect cells have identified a high level of glycosylation on the protein’s surface. Here we used IBV propagated in embryonated hens’ eggs to explore the glycan profile of viruses derived from infection in cells of the natural host, chickens. We identified multiple glycan types on the surface of the protein and found a strain-specific dependence on complex glycans for recognition of the S2 subunit by a monoclonal antibody in vitro, with no effect on viral replication following the chemical inhibition of complex glycosylation. Virus neutralization by monoclonal or polyclonal antibodies was not affected. Following analysis of predicted glycosylation sites for the S protein of four IBV strains, we confirmed glycosylation at 18 sites by mass spectrometry for the pathogenic laboratory strain M41-CK. Further characterization revealed heterogeneity among the glycans present at six of these sites, indicating a difference in the glycan profile of individual S proteins on the IBV virion. These results demonstrate a non-specific role for complex glycans in IBV replication, with an indication of an involvement in antibody recognition but not neutralisation.
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Affiliation(s)
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Sarah Keep
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
| | - Paul Britton
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
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5
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Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2. Biophys J 2021; 120:2902-2913. [PMID: 33705760 PMCID: PMC7939993 DOI: 10.1016/j.bpj.2021.02.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long molecular dynamics simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. The roles of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, in which the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intracommunication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.
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6
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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7
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Chakraborty S, Berndsen ZT, Hengartner NW, Korber BT, Ward AB, Gnanakaran S. Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail. iScience 2020; 23:101836. [PMID: 33319171 PMCID: PMC7724196 DOI: 10.1016/j.isci.2020.101836] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/22/2020] [Accepted: 11/17/2020] [Indexed: 01/09/2023] Open
Abstract
Dense surface glycosylation on the HIV-1 envelope (Env) protein acts as a shield from the adaptive immune system. However, the molecular complexity and flexibility of glycans make experimental studies a challenge. Here we have integrated high-throughput atomistic modeling of fully glycosylated HIV-1 Env with graph theory to capture immunologically important features of the shield topology. This is the first complete all-atom model of HIV-1 Env SOSIP glycan shield that includes both oligomannose and complex glycans, providing physiologically relevant insights of the glycan shield. This integrated approach including quantitative comparison with cryo-electron microscopy data provides hitherto unexplored details of the native shield architecture and its difference from the high-mannose glycoform. We have also derived a measure to quantify the shielding effect over the antigenic protein surface that defines regions of relative vulnerability and resilience of the shield and can be harnessed for rational immunogen design.
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Affiliation(s)
- Srirupa Chakraborty
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Zachary T. Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicolas W. Hengartner
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette T. Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - S. Gnanakaran
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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8
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Stewart TJ, Takahashi K, Xu N, Prakash A, Brown R, Raska M, Renfrow MB, Novak J. Quantitative assessment of successive carbohydrate additions to the clustered O-glycosylation sites of IgA1 by glycosyltransferases. Glycobiology 2020; 31:540-556. [PMID: 33295603 DOI: 10.1093/glycob/cwaa111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/12/2022] Open
Abstract
Mucin-type O-glycosylation occurs on many proteins that transit the Golgi apparatus. These glycans impact structure and function of many proteins and have important roles in cellular biosynthetic processes, signaling and differentiation. Although recent technological advances have enhanced our ability to profile glycosylation of glycoproteins, limitations in the understanding of the biosynthesis of these glycan structures remain. Some of these limitations stem from the difficulty to track the biosynthetic process of mucin-type O-glycosylation, especially when glycans occur in dense clusters in repeat regions of proteins, such as the mucins or immunoglobulin A1 (IgA1). Here, we describe a series of nano-liquid chromatography (LC)-mass spectrometry (MS) analyses that demonstrate the range of glycosyltransferase enzymatic activities involved in the biosynthesis of clustered O-glycans on IgA1. By utilizing nano-LC-MS relative quantitation of in vitro reaction products, our results provide unique insights into the biosynthesis of clustered IgA1 O-glycans. We have developed a workflow to determine glycoform-specific apparent rates of a human UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltrasnfersase (GalNAc-T EC 2.4.1.41) and demonstrated how pre-existing glycans affect subsequent activity of glycosyltransferases, such as core 1 galactosyltransferase and α2,3- and α2,6-specific sialyltransferases, in successive additions in the biosynthesis of clustered O-glycans. In the context of IgA1, these results have potential to provide insight into the molecular mechanisms implicated in the pathogenesis of IgA nephropathy, an autoimmune renal disease involving aberrant IgA1 O-glycosylation. In a broader sense, these methods and workflows are applicable to the studies of the concerted and competing functions of other glycosyltransferases that initiate and extend mucin-type core 1 clustered O-glycosylation.
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Affiliation(s)
- Tyler J Stewart
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, KAUL 524, Birmingham, AL 35294, USA
| | - Kazuo Takahashi
- Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake, Aichi, Toyoake 470-1192, Japan.,Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
| | - Nuo Xu
- Department of Management, Information Systems & Quantitative Methods, 710 13th Street South, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Amol Prakash
- Optys Tech Corporation, Shrewsbury, MA 01545, USA
| | - Rhubell Brown
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
| | - Milan Raska
- Department of Immunology, Palacky University and University Hospital, Hnevotinska 3, Olomouc 775 15, Czech Republic
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, KAUL 524, Birmingham, AL 35294, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
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9
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Wei Q, Hargett AA, Knoppova B, Duverger A, Rawi R, Shen CH, Farney SK, Hall S, Brown R, Keele BF, Heath SL, Saag MS, Kutsch O, Chuang GY, Kwong PD, Moldoveanu Z, Raska M, Renfrow MB, Novak J. Glycan Positioning Impacts HIV-1 Env Glycan-Shield Density, Function, and Recognition by Antibodies. iScience 2020; 23:101711. [PMID: 33205023 PMCID: PMC7649354 DOI: 10.1016/j.isci.2020.101711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/12/2020] [Accepted: 10/16/2020] [Indexed: 11/24/2022] Open
Abstract
HIV-1 envelope (Env) N-glycosylation impact virus-cell entry and immune evasion. How each glycan interacts to shape the Env-protein-sugar complex and affects Env function is not well understood. Here, analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation sites affected the Env structure at distant locations and had a ripple effect on Env-wide glycan processing, virus infectivity, antibody recognition, and virus neutralization. Specifically, the N262 glycan, although not in the CD4-binding site, modulated Env binding to the CD4 receptor, affected Env recognition by several glycan-dependent neutralizing antibodies, and altered site-specific glycosylation heterogeneity, with, for example, N448 displaying limited glycan processing. Molecular-dynamic simulations visualized differences in glycan density and how specific oligosaccharide positions can move to compensate for a glycan loss. This study demonstrates how changes in individual glycans can alter molecular dynamics, processing, and function of the Env-glycan shield. Two HIV-1 envelopes (Env) that differ in N-glycan composition were investigated Changes in N-glycosylation had ripple effect on Env-wide glycan processing Glycan changes impacted virus infectivity, antibody binding, and neutralization These data revealed a functional role of glycan clusters in Env glycan shield
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Affiliation(s)
- Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Audra A Hargett
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbora Knoppova
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Alexandra Duverger
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - S Katie Farney
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stacy Hall
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Rhubell Brown
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olaf Kutsch
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zina Moldoveanu
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
| | - Milan Raska
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA.,Department of Immunology, Palacky University Olomouc, Olomouc, Czech Republic
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA
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10
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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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11
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Ohyama Y, Nakajima K, Renfrow MB, Novak J, Takahashi K. Mass spectrometry for the identification and analysis of highly complex glycosylation of therapeutic or pathogenic proteins. Expert Rev Proteomics 2020; 17:275-296. [PMID: 32406805 DOI: 10.1080/14789450.2020.1769479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Protein glycosylation influences characteristics such as folding, stability, protein interactions, and solubility. Therefore, glycan moieties of therapeutic proteins and proteins that are likely associated with disease pathogenesis should be analyzed in-depth, including glycan heterogeneity and modification sites. Recent advances in analytical methods and instrumentation have enabled comprehensive characterization of highly complex glycosylated proteins. AREA COVERED The following aspects should be considered when analyzing glycosylated proteins: sample preparation, chromatographic separation, mass spectrometry (MS) and fragmentation methods, and bioinformatics, such as software solutions for data analyses. Notably, analysis of glycoproteins with heavily sialylated glycans or multiple glycosylation sites requires special considerations. Here, we discuss recent methodological advances in MS that provide detailed characterization of heterogeneous glycoproteins. EXPERT OPINION As characterization of complex glycosylated proteins is still analytically challenging, the function or pathophysiological significance of these proteins is not fully understood. To reproducibly produce desired forms of therapeutic glycoproteins or to fully elucidate disease-specific patterns of protein glycosylation, a highly reproducible and robust analytical platform(s) should be established. In addition to advances in MS instrumentation, optimization of analytical and bioinformatics methods and utilization of glycoprotein/glycopeptide standards is desirable. Ultimately, we envision that an automated high-throughput MS analysis will provide additional power to clinical studies and precision medicine.
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Affiliation(s)
- Yukako Ohyama
- Department of Nephrology, Fujita Health University School of Medicine , Toyoake, Japan.,Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine , Toyoake, Japan
| | - Kazuki Nakajima
- Center for Research Promotion and Support, Fujita Health University , Toyoake, Japan
| | - Matthew B Renfrow
- Departments of Biochemistry and Molecular Genetics and Microbiology, University of Alabama at Birmingham , Birmingham, AL, USA
| | - Jan Novak
- Departments of Biochemistry and Molecular Genetics and Microbiology, University of Alabama at Birmingham , Birmingham, AL, USA
| | - Kazuo Takahashi
- Department of Nephrology, Fujita Health University School of Medicine , Toyoake, Japan.,Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine , Toyoake, Japan.,Departments of Biochemistry and Molecular Genetics and Microbiology, University of Alabama at Birmingham , Birmingham, AL, USA
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Watanabe Y, Berndsen ZT, Raghwani J, Seabright GE, Allen JD, Pybus OG, McLellan JS, Wilson IA, Bowden TA, Ward AB, Crispin M. Vulnerabilities in coronavirus glycan shields despite extensive glycosylation. Nat Commun 2020; 11:2688. [PMID: 32461612 PMCID: PMC7253482 DOI: 10.1038/s41467-020-16567-0] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. Vaccine development focuses on the principal target of the neutralizing humoral immune response, the spike (S) glycoprotein. Coronavirus S proteins are extensively glycosylated, encoding around 66-87 N-linked glycosylation sites per trimeric spike. Here, we reveal a specific area of high glycan density on MERS S that results in the formation of oligomannose-type glycan clusters, which were absent on SARS and HKU1 CoVs. We provide a comparison of the global glycan density of coronavirus spikes with other viral proteins including HIV-1 envelope, Lassa virus glycoprotein complex, and influenza hemagglutinin, where glycosylation plays a known role in shielding immunogenic epitopes. Overall, our data reveal how organisation of glycosylation across class I viral fusion proteins influence not only individual glycan compositions but also the immunological pressure across the protein surface.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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13
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Proteins mimicking epitope of HIV-1 virus neutralizing antibody induce virus-neutralizing sera in mice. EBioMedicine 2020; 47:247-256. [PMID: 31544770 PMCID: PMC6796546 DOI: 10.1016/j.ebiom.2019.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Accepted: 07/04/2019] [Indexed: 01/26/2023] Open
Abstract
Background The development of an effective vaccine preventing HIV-1 infection is hindered by the enormous antigenic variability and unique biochemical and immunological properties of HIV-1 Env glycoprotein, the most promising target for HIV-1 neutralizing antibody. Functional studies of rare elite neutralizers led to the discovery of broadly neutralizing antibodies. Methods We employed a highly complex combinatorial protein library derived from a 5 kDa albumin-binding domain scaffold, fused with support protein of total 38 kDa, to screen for binders of broadly neutralizing antibody VRC01 paratope. The most specific binders were used for immunization of experimental mice to elicit Env-specific antibodies and to test their neutralization activity using a panel of HIV-1 clade C and B pseudoviruses. Findings Three most specific binders designated as VRA017, VRA019, and VRA177 exhibited high specificity to VRC01 antibody. Immunized mice produced Env-binding antibodies which neutralize eight of twelve HIV-1 Tier 2 pseudoviruses. Molecular modelling revealed a shape complementarity between VRA proteins and a part of VRC01 gp120 interacting surface. Interpretation This strategy based on the identification of protein replicas of broadly neutralizing antibody paratope represents a novel approach in HIV-1 vaccine development. This approach is not affected by low immunogenicity of neutralization-sensitive epitopes, variability, and unique biochemical properties of HIV-1 Env used as a crucial antigen in the majority of contemporary tested vaccines. Fund Czech Health Research Council 15-32198A, Ministry of Health, Czech Republic.
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Hargett AA, Renfrow MB. Glycosylation of viral surface proteins probed by mass spectrometry. Curr Opin Virol 2019; 36:56-66. [PMID: 31202133 PMCID: PMC7102858 DOI: 10.1016/j.coviro.2019.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
Abstract
Glycosylation is a common and biologically significant post-translational modification that is found on numerous virus surface proteins (VSPs). Many of these glycans affect virulence through modulating virus receptor binding, masking antigenic sites, or by stimulating the host immune response. Mass spectrometry (MS) has arisen as a pivotal technique for the characterization of VSP glycosylation. This review will cover how MS-based analyses, such as released glycan profiles, glycan site localization, site-occupancy, and site-specific heterogeneity, are being utilized to map VSP glycosylation. Furthermore, this review will provide information on how MS glycoprofiling data are being used in conjunction with molecular and structural experiments to provide a better understanding of the role of specific glycans in VSP function.
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Affiliation(s)
- Audra A Hargett
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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