1
|
Sun Y, Zhu Y, Zhang P, Sheng S, Guan Z, Cong Y. Hemagglutinin glycosylation pattern-specific effects: implications for the fitness of H9.4.2.5-branched H9N2 avian influenza viruses. Emerg Microbes Infect 2024; 13:2364736. [PMID: 38847071 PMCID: PMC11182062 DOI: 10.1080/22221751.2024.2364736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/02/2024] [Indexed: 06/16/2024]
Abstract
Since 2007, h9.4.2.5 has emerged as the most predominant branch of H9N2 avian influenza viruses (AIVs) that affects the majority of the global poultry population. The spread of this viral branch in vaccinated chicken flocks has not been considerably curbed despite numerous efforts. The evolutionary fitness of h9.4.2.5-branched AIVs must consequently be taken into consideration. The glycosylation modifications of hemagglutinin (HA) play a pivotal role in regulating the balance between receptor affinity and immune evasion for influenza viruses. Sequence alignment showed that five major HA glycosylation patterns have evolved over time in h9.4.2.5-branched AIVs. Here, we compared the adaptive phenotypes of five virus mutants with different HA glycosylation patterns. According to the results, the mutant with 6 N-linked glycans displayed the best acid and thermal stability and a better capacity for multiplication, although having a relatively lower receptor affinity than 7 glycans. The antigenic profile between the five mutants revealed a distinct antigenic distance, indicating that variations in glycosylation level have an impact on antigenic drift. These findings suggest that changes in the number of glycans on HA can not only modulate the receptor affinity and antigenicity of H9N2 AIVs, but also affect their stability and multiplication. These adaptive phenotypes may underlie the biological basis for the dominant strain switchover of h9.4.2.5-branched AIVs. Overall, our study provides a systematic insight into how changes in HA glycosylation patterns regulate the evolutionary fitness and epidemiological dominance drift of h9.4.2.5-branched H9N2 AIVs, which will be of great benefit for the glycosylation-dependent vaccine design.
Collapse
Affiliation(s)
- Yixue Sun
- Department of Policies and Regulations, Changchun University, Changchun, People’s Republic of China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanting Zhu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengju Zhang
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, People’s Republic of China
| | - Shouzhi Sheng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhenhong Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanlong Cong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
2
|
Arigoni-Affolter I, Losfeld ME, Hennig R, Rapp E, Aebi M. A hierarchical structure in the N-glycosylation process governs the N-glycosylation output: prolonged cultivation induces glycoenzymes expression variations that are reflected in the cellular N-glycome but not in the protein and site-specific glycoprofile of CHO cells. Glycobiology 2024; 34:cwae045. [PMID: 38938083 PMCID: PMC11231950 DOI: 10.1093/glycob/cwae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/18/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
N-glycosylation is a central component in the modification of secretory proteins. One characteristic of this process is a heterogeneous output. The heterogeneity is the result of both structural constraints of the glycoprotein as well as the composition of the cellular glycosylation machinery. Empirical data addressing correlations between glycosylation output and glycosylation machinery composition are seldom due to the low abundance of glycoenzymes. We assessed how differences in the glycoenzyme expression affected the N-glycosylation output at a cellular as well as at a protein-specific level. Our results showed that cellular N-glycome changes could be correlated with the variation of glycoenzyme expression, whereas at the protein level differential responses to glycoenzymes alterations were observed. We therefore identified a hierarchical structure in the N-glycosylation process: the enzyme levels in this complex pathway determine its capacity (reflected in the N-glycome), while protein-specific parameters determine the glycosite-specificity. What emerges is a highly variable and adaptable protein modification system that represents a hallmark of eukaryotic cells.
Collapse
Affiliation(s)
- Ilaria Arigoni-Affolter
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 4, 8049 Zürich, Switzerland
| | - Marie-Estelle Losfeld
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 4, 8049 Zürich, Switzerland
| | - René Hennig
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse, 39106 Magdeburg, Germany
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 4, 8049 Zürich, Switzerland
| |
Collapse
|
3
|
Hiono T, Sakaue H, Tomioka A, Kaji H, Sasaki M, Orba Y, Sawa H, Kuno A. Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains. J Proteome Res 2024; 23:1408-1419. [PMID: 38536229 DOI: 10.1021/acs.jproteome.3c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted public health globally. As the glycosylation of viral envelope glycoproteins is strongly associated with their immunogenicity, intensive studies have been conducted on the glycans of the glycoprotein of SARS-CoV-2, the spike (S) protein. Here, we conducted intensive glycoproteomic analyses of the SARS-CoV-2 S protein of ancestral and γ-variant strains using a combinatorial approach with two different technologies: mass spectrometry (MS) and lectin microarrays (LMA). Our unique MS1-based glycoproteomic technique, Glyco-RIDGE, in addition to MS2-based Byonic search, identified 1448 (ancestral strain) and 1785 (γ-variant strain) site-specific glycan compositions, respectively. Asparagine at amino acid position 20 (N20) is mainly glycosylated within two successive potential glycosylation sites, N17 and N20, of the γ-variant S protein; however, we found low-frequency glycosylation at N17. Our novel approaches, glycostem mapping and glycoleaf scoring, also illustrate the moderately branched/extended, highly fucosylated, and less sialylated natures of the glycoforms of S proteins. Subsequent LMA analysis emphasized the intensive end-capping of glycans by Lewis fucoses, which complemented the glycoproteomic features. These results illustrate the high-resolution glycoproteomic features of the SARS-CoV-2 S protein, contributing to vaccine design and understanding of viral protein synthesis.
Collapse
Affiliation(s)
- Takahiro Hiono
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Hiroaki Sakaue
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Azusa Tomioka
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Hiroyuki Kaji
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Michihito Sasaki
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Yasuko Orba
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| |
Collapse
|
4
|
Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
Collapse
Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
5
|
Wong TL, Mooney BP, Cavallero GJ, Guan M, Li L, Zaia J, Wan XF. Glycoproteomic Analyses of Influenza A Viruses Using timsTOF Pro MS. J Proteome Res 2023; 22:62-77. [PMID: 36480915 DOI: 10.1021/acs.jproteome.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-Linked glycosylation in hemagglutinin and neuraminidase glycoproteins of influenza viruses affects antigenic and receptor binding properties, and precise analyses of site-specific glycoforms in these proteins are critical in understanding the antigenic and immunogenic properties of influenza viruses. In this study, we developed a glycoproteomic approach by using a timsTOF Pro mass spectrometer (MS) to determine the abundance and heterogeneity of site-specific glycosylation for influenza glycoproteins. Compared with a Q Exactive HF MS, the timsTOF Pro MS method without the hydrophilic interaction liquid chromatography column enrichment achieved similar glycopeptide coverage and quantities but was more effective in identifying low-abundance glycopeptides. We quantified the distributions of intact site-specific glycopeptides in hemagglutinin of A/chicken/Wuxi/0405005/2013 (H7N9) and A/mute swan/Rhode Island/A00325125/2008 (H7N3). Results showed that hemagglutinin for both viruses had complex N-glycans at N22, N38, N240, and N483 but only high-mannose glycans at N411 and, however, that the type and quantities of glycans were distinct between these viruses. Collisional cross section (CCS) provided by the ion mobility spectrometry from the timsTOF Pro MS data differentiated sialylation linkages of the glycopeptides. In summary, timsTOF Pro MS method can quantify intact site-specific glycans for influenza glycoproteins without enrichment and thus facilitate influenza vaccine development and production.
Collapse
Affiliation(s)
- Tin Long Wong
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Brian P Mooney
- Department of Biochemistry and Charles W. Gehrke Proteomics Center, University of Missouri, Columbia, Missouri65211, United States
| | - Gustavo J Cavallero
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Minhui Guan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia30302, United States
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States.,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri65211, United States
| |
Collapse
|
6
|
Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS CENTRAL SCIENCE 2022; 8:1646-1663. [PMID: 36589893 PMCID: PMC9801513 DOI: 10.1021/acscentsci.2c00981] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 05/28/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from convalescent human donor, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
Collapse
Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Julia Lederhofer
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Yaroslav Tsybovsky
- Electron
Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
Sponsored by the National Cancer Institute, Frederick, Maryland21702, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California92037, United States
| | - Masaru Kanekiyo
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.02.502576. [PMID: 35982676 PMCID: PMC9387122 DOI: 10.1101/2022.08.02.502576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
Collapse
Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States,Corresponding author.
| |
Collapse
|
9
|
Campos D, Girgis M, Sanda M. Site-specific glycosylation of SARS-CoV-2: Big challenges in mass spectrometry analysis. Proteomics 2022; 22:e2100322. [PMID: 35700310 PMCID: PMC9349404 DOI: 10.1002/pmic.202100322] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022]
Abstract
Glycosylation of viral proteins is required for the progeny formation and infectivity of virtually all viruses. It is increasingly clear that distinct glycans also play pivotal roles in the virus's ability to shield and evade the host's immune system. Recently, there has been a great advancement in structural identification and quantitation of viral glycosylation, especially spike proteins. Given the ongoing pandemic and the high demand for structure analysis of SARS-CoV-2 densely glycosylated spike protein, mass spectrometry methodologies have been employed to accurately determine glycosylation patterns. There are still many challenges in the determination of site-specific glycosylation of SARS-CoV-2 viral spike protein. This is compounded by some conflicting results regarding glycan site occupancy and glycan structural characterization. These are probably due to differences in the expression systems, form of expressed spike glycoprotein, MS methodologies, and analysis software. In this review, we recap the glycosylation of spike protein and compare among various studies. Also, we describe the most recent advancements in glycosylation analysis in greater detail and we explain some misinterpretation of previously observed data in recent publications. Our study provides a comprehensive view of the spike protein glycosylation and highlights the importance of consistent glycosylation determination.
Collapse
Affiliation(s)
- Diana Campos
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
| | - Michael Girgis
- Department of BioengineeringVolgenau School of Engineering and ComputingGeorge Mason UniversityFairfaxVirginiaUSA
| | - Miloslav Sanda
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
- Clinical and Translational Glycoscience Research CenterGeorgetown UniversityWashingtonDCUSA
| |
Collapse
|
10
|
Mirgorodskaya E, Dransart E, Shafaq-Zadah M, Roderer D, Sihlbom C, Leffler H, Johannes L. Site-specific N-glycan profiles of α 5 β 1 integrin from rat liver. Biol Cell 2022; 114:160-176. [PMID: 35304921 DOI: 10.1111/boc.202200017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/03/2021] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND INFORMATION Like most other cell surface proteins, α5 β1 integrin is glycosylated, which is required for its various activities in ways that mostly remain to be determined. RESULTS Here, we have established the first comprehensive site-specific glycan map of α5 β1 integrin that was purified from a natural source, i.e., rat liver. This analysis revealed striking site selective variations in glycan composition. Complex bi, tri or tetraantennary N-glycans were predominant at various proportions at most potential N-glycosylation sites. A few of these sites were non-glycosylated or contained high mannose or hybrid glycans, indicating that early N-glycan processing was hindered. Almost all complex N-glycans had fully galactosylated and sialylated antennae. Moderate levels of core fucosylation and high levels of O-acetylation of NeuAc residues were observed at certain sites. An O-linked HexNAc was found in an EGF-like domain of β1 integrin. The extensive glycan information that results from our study was projected onto a map of α5 β1 integrin that was obtained by homology modeling. We have used this model for the discussion of how glycosylation might be used in the functional cycle of α5 β1 integrin. A striking example concerns the involvement of glycan-binding galectins in the regulation of the molecular homeostasis of glycoproteins at the cell surface through the formation of lattices or endocytic pits according to the glycolipid-lectin (GL-Lect) hypothesis. CONCLUSION We expect that the glycoproteomics data of the current study will serve as a resource for the exploration of structural mechanisms by which glycans control α5 β1 integrin activity and endocytic trafficking. SIGNIFICANCE Glycosylation of α5 β1 integrin has been implicated in multiple aspects of integrin function and structure. Yet, detailed knowledge of its glycosylation, notably the specific sites of glycosylation, is lacking. Furthermore, the α5 β1 integrin preparation that was analyzed here is from a natural source, which is of importance as there is not a lot of literature in the field about the glycosylation of 'native' glycoproteins. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
| | - Estelle Dransart
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, 26 rue d'Ulm, 75248, Paris, Cedex, 05, France
| | - Massiullah Shafaq-Zadah
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, 26 rue d'Ulm, 75248, Paris, Cedex, 05, France
| | - Daniel Roderer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin, 13125, Germany
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Hakon Leffler
- Section MIG (Microbiology, Immunology, Glycobiology), Department of Laboratory Medicine, Lund University, Sweden
| | - Ludger Johannes
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, 26 rue d'Ulm, 75248, Paris, Cedex, 05, France
| |
Collapse
|
11
|
Aberrant Cellular Glycosylation May Increase the Ability of Influenza Viruses to Escape Host Immune Responses through Modification of the Viral Glycome. mBio 2022; 13:e0298321. [PMID: 35285699 PMCID: PMC9040841 DOI: 10.1128/mbio.02983-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Individuals with metabolic dysregulation of cellular glycosylation often experience severe influenza disease, with a poor immune response to the virus and low vaccine efficacy. Here, we investigate the consequences of aberrant cellular glycosylation for the glycome and the biology of influenza virus. We transiently induced aberrant N-linked glycosylation in cultured cells with an oligosaccharyltransferase inhibitor, NGI-1. Cells treated with NGI-1 produced morphologically unaltered viable influenza virus with sequence-neutral glycosylation changes (primarily reduced site occupancy) in the hemagglutinin and neuraminidase proteins. Hemagglutinin with reduced glycan occupancy required a higher concentration of surfactant protein D (an important innate immunity respiratory tract collectin) for inhibition compared to that with normal glycan occupancy. Immunization of mice with NGI-1-treated virus significantly reduced antihemagglutinin and antineuraminidase titers of total serum antibody and reduced hemagglutinin protective antibody responses. Our data suggest that aberrant cellular glycosylation may increase the risk of severe influenza as a result of the increased ability of glycome-modified influenza viruses to evade the immune response.
Collapse
|
12
|
Hiono T, Kuno A. Glycan Profiling of Viral Glycoproteins with the Lectin Microarray. Methods Mol Biol 2022; 2556:59-68. [PMID: 36175627 DOI: 10.1007/978-1-0716-2635-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recently, structural analyses on the glycans attached to viral surface proteins have been intensively conducted since previous studies demonstrated that glycoform of the viral glycoproteins is closely related to their immunogenicity as vaccine antigens. Although mass spectrometric approach is a gold standard for the glycoproteomic analysis of viral glycoproteins, lectin microarray (LMA) is regarded as an alternative method for analyzing glycan attached to viruses. The previous studies demonstrated that LMA provides highly sensitive and straightforward platforms for the glycoproteomic analyses of viral glycans. Here, two methods, antibody-overlay method, and direct-labeling method, for profiling glycoforms of viral glycoprotein using LMA are described.
Collapse
Affiliation(s)
- Takahiro Hiono
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Ibaraki, Japan.
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan.
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Ibaraki, Japan
| |
Collapse
|
13
|
White MR, Nikolaidis NM, McCormack F, Crouch EC, Hartshorn KL. Viral Evasion of Innate Immune Defense: The Case of Resistance of Pandemic H1N1 Influenza A Virus to Human Mannose-Binding Proteins. Front Microbiol 2021; 12:774711. [PMID: 34956139 PMCID: PMC8692257 DOI: 10.3389/fmicb.2021.774711] [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] [Received: 09/12/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Mannose-binding lectins effectively inhibit most seasonal strains of influenza A virus and contribute to the innate host defense vs. these viruses. In contrast, pandemic IAV strains are largely resistant to these lectins, likely contributing to increased spread and worse outcomes. In this paper, we evaluated the inhibition of IAV by mannose-binding lectins of human, bacterial, and fungal origin to understand and possibly increase activity vs. the pandemic IAV. A modified version of the human surfactant protein D (SP-D) neck and carbohydrate recognition domain (NCRD) with combinatorial substitutions at the 325 and 343 positions, previously shown to inhibit pandemic H3N2 IAV in vitro and in vivo, and to inhibit pandemic H1N1 in vitro, failed to protect mice from pandemic H1N1 in vivo in the current study. We attempted a variety of maneuvers to improve the activity of the mutant NCRDs vs. the 2009 pandemic H1N1, including the formation of full-length SP-D molecules containing the mutant NCRD, cross-linking of NCRDs through the use of antibodies, combining SP-D or NCRDs with alpha-2-macroglobulin, and introducing an additional mutation to the double mutant NCRD. None of these substantially increased the antiviral activity for the pandemic H1N1. We also tested the activity of bacterial and algal mannose-binding lectins, cyanovirin, and griffithsin, against IAV. These had strong activity against seasonal IAV, which was largely retained against pandemic H1N1. We propose mechanisms to account for differences in activity of SP-D constructs against pandemic H3N2 and H1N1, and for differences in activity of cyanovirin vs. SP-D constructs.
Collapse
Affiliation(s)
- Mitchell R. White
- Department of Medicine, Section of Hematology and Oncology, School of Medicine, Boston University, Boston, MA, United States
| | - Nikolaos M. Nikolaidis
- Division of Pulmonary and Critical Care Medicine, University of Cincinnati, Cincinnati, OH, United States,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Francis McCormack
- Division of Pulmonary and Critical Care Medicine, University of Cincinnati, Cincinnati, OH, United States,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Erika C. Crouch
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kevan L. Hartshorn
- Department of Medicine, Section of Hematology and Oncology, School of Medicine, Boston University, Boston, MA, United States,*Correspondence: Kevan L. Hartshorn,
| |
Collapse
|
14
|
Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
Collapse
Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
| |
Collapse
|
15
|
Roberts DS, Mann M, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry. J Am Chem Soc 2021; 143:12014-12024. [PMID: 34328324 PMCID: PMC8353889 DOI: 10.1021/jacs.1c02713] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry, and the S protein glycosylation plays key roles in altering the viral binding/function and infectivity. However, the molecular structures and glycan heterogeneity of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report the complete structural elucidation of intact O-glycan proteoforms through a hybrid native and denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR)-MS. Native top-down TIMS-MS/MS separates the protein conformers of the S-RBD to reveal their gas-phase structural heterogeneity, and top-down FTICR-MS/MS provides in-depth glycoform analysis for unambiguous identification of the glycan structures and their glycosites. A total of eight O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that this hybrid top-down MS approach can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants as well as other O-glycoproteins in general.
Collapse
Affiliation(s)
- David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Morgan Mann
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Allan R Brasier
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| |
Collapse
|
16
|
Wang M, Shajahan A, Pepi LE, Azadi P, Zaia J. Glycoproteomic Sample Processing, LC-MS, and Data Analysis Using GlycReSoft. Curr Protoc 2021; 1:e84. [PMID: 33761173 DOI: 10.1002/cpz1.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Identification of N- and O-glycosylation on specific sites of proteins, along with glycan structural information, is necessary to determine the roles glycoproteins play in normal and pathologic cellular functions. Because such glycosylation is macro- and micro-heterogeneous and alters the dissociation behavior of glycopeptides, specific sample preparation, mass spectrometry, and data analysis techniques are required. Advanced tandem mass spectrometry-based glycoproteomics coupled with powerful data mining algorithms are key elements for characterization of protein glycosylation. This article includes the detailed, streamlined sample preparation method for liquid chromatography-mass spectrometry data acquisition and subsequent bioinformatics-based data annotation using the publicly available GlycReSoft program for highly efficient identification and quantification of glycoprotein glycosylation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Characterization of glycans and site occupancy on purified glycoprotein Support Protocol 1: In-gel digestion of glycoproteins Support Protocol 2: Detection of glycoproteins from cells/tissue through glycopeptide enrichment Basic Protocol 2: Acquisition of glycopeptides through high-resolution nano-LC-MS/MS Basic Protocol 3: Identification and quantification of glycopeptides using GlycReSoft.
Collapse
Affiliation(s)
- Meizhe Wang
- Department of Biochemistry, Boston University, Boston, Massachusetts
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Lauren E Pepi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Joseph Zaia
- Department of Biochemistry, Boston University, Boston, Massachusetts.,Bioinformatics Program, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts
| |
Collapse
|
17
|
Li J, Liu S, Gao Y, Tian S, Yang Y, Ma N. Comparison of N-linked glycosylation on hemagglutinins derived from chicken embryos and MDCK cells: a case of the production of a trivalent seasonal influenza vaccine. Appl Microbiol Biotechnol 2021; 105:3559-3572. [PMID: 33937925 PMCID: PMC8088833 DOI: 10.1007/s00253-021-11247-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/28/2022]
Abstract
Abstract N-linked glycosylation plays critical roles in folding, receptor binding, and immunomodulating of hemagglutinin (HA), the main antigen in influenza vaccines. Chicken embryos are the predominant production host for influenza vaccines, but Madin-Darby canine kidney (MDCK) cells have emerged as an important alternative host. In this study, we compared glycosylation patterns, including the occupancy of potential glycosylation sites and the distribution of different glycans, on the HAs of three strains of influenza viruses for the production a trivalent seasonal flu vaccine for the 2015-2016 Northern Hemisphere season (i.e., A/California/7/2009 (H1N1) X179A, A/Switzerland/9715293/2013 (H3N2) NIB-88, and B/Brisbane/60/2008 NYMC BX-35###). Of the 8, 12, and 11 potential glycosylation sites on the HAs of H1N1, H3N2, and B strains, respectively, most were highly occupied. For the H3N2 and B strains, MDCK-derived HAs contained more sites being partially occupied (<95%) than embryo-derived HAs. A highly sensitive glycan assay was developed where 50 different glycans were identified, which was more than what has been reported previously, and their relative abundance was quantified. In general, MDCK-derived HAs contain more glycans of higher molecular weight. High-mannose species account for the most abundant group of glycans, but at a lower level as compared to those reported in previous studies, presumably due to that lower abundance, complex structure glycans were accounted for in this study. The different glycosylation patterns between MDCK- and chicken embryo-derived HAs may help elucidate the role of glycosylation on the function of influenza vaccines. Key points • For the H3N2 and B strains, MDCK-derived HAs contained more partially (<95%) occupied glycosylation sites. • MDCK-derived HAs contained more glycans of higher molecular weight. • A systematic comparison of glycosylation on HAs used for trivalent seasonal flu vaccines was conducted. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11247-5.
Collapse
Affiliation(s)
- Jingqi Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China
| | - Sixu Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China
| | - Yanlin Gao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China.,School of Computing, Urban Sciences Building, Newcastle University, 1 Science Square, Newcastle Helix, Newcastle upon Tyne, NE4 5TG, UK
| | - Shuaishuai Tian
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China
| | - Yu Yang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China.
| | - Ningning Ma
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China.
| |
Collapse
|
18
|
Matoba Y, Sato Y, Oda K, Hatori Y, Morimoto K. Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity. J Biol Chem 2021; 296:100698. [PMID: 33895142 PMCID: PMC8166773 DOI: 10.1016/j.jbc.2021.100698] [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] [Received: 11/09/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 01/08/2023] Open
Abstract
Homologues of the Oscillatoria agardhii agglutinin (OAA) lectins contain a sequence repeat of ∼66 amino acids, with the number of tandem repeats varying across family members. OAA homologues bind high-mannose glycans on viral surface proteins, thereby interfering with viral entry into host cells. As such, OAA homologues have potential utility as antiviral agents, but a more detailed understanding of their structure–function relationships would enable us to develop improved constructs. Here, we determined the X-ray crystal structure of free and glycan-bound forms of Pseudomonas taiwanensis lectin (PTL), an OAA-family lectin consisting of two tandem repeats. Like other OAA-family lectins, PTL exhibited a β-barrel-like structure with two symmetrically positioned glycan-binding sites at the opposite ends of the barrel. Upon glycan binding, the conformation of PTL undergoes a more significant change than expected from previous OAA structural analysis. Moreover, the electron density of the bound glycans suggested that the binding affinities are different at the two binding sites. Next, based on analysis of these structures, we used site-specific mutagenesis to create PTL constructs expected to increase the population with a conformation suitable for glycan binding. The engineered PTLs were examined for their antiviral activity against the influenza virus. Interestingly, some exhibited stronger activity compared with that of the parent PTL. We propose that our approach is effective for the generation of potential microbicides with enhanced antiviral activity.
Collapse
Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Yuichiro Sato
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Kosuke Oda
- Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuta Hatori
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Kinjiro Morimoto
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan.
| |
Collapse
|
19
|
Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021; 49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.
Collapse
Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| |
Collapse
|
20
|
Mathew C, Weiß RG, Giese C, Lin CW, Losfeld ME, Glockshuber R, Riniker S, Aebi M. Glycan-protein interactions determine kinetics of N-glycan remodeling. RSC Chem Biol 2021; 2:917-931. [PMID: 34212152 PMCID: PMC8207518 DOI: 10.1039/d1cb00019e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A hallmark of N-linked glycosylation in the secretory compartments of eukaryotic cells is the sequential remodeling of an initially uniform oligosaccharide to a site-specific, heterogeneous ensemble of glycostructures on mature proteins. To understand site-specific processing, we used protein disulfide isomerase (PDI), a model protein with five glycosylation sites, for molecular dynamics (MD) simulations and compared the result to a biochemical in vitro analysis with four different glycan processing enzymes. As predicted by an analysis of the accessibility of the N-glycans for their processing enzymes derived from the MD simulations, N-glycans at different glycosylation sites showed different kinetic properties for the processing enzymes. In addition, altering the tertiary structure of the glycoprotein PDI affected its N-glycan remodeling in a site-specific way. We propose that the observed differential N-glycan reactivities depend on the surrounding protein tertiary structure and lead to different glycan structures in the same protein through kinetically controlled processing pathways. Atomistic glycoprotein simulations reveal a site-specific availability of glycan substrates in time-resolved mass spectrometry of maturating enzyme kinetics.![]()
Collapse
Affiliation(s)
- Corina Mathew
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - R Gregor Weiß
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Christoph Giese
- Institute of Molecular Biology & Biophysics, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland .,Functional Genomics Center Zürich 8057 Zürich Switzerland
| | - Marie-Estelle Losfeld
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology & Biophysics, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich 8093 Zürich Switzerland
| |
Collapse
|
21
|
Wang M, Shajahan A, Pepi LE, Azadi P, Zaia J. Glycoproteomic Sample Processing, LC-MS, and Data Analysis Using GlycReSoft. Curr Protoc 2021. [PMID: 33761173 DOI: 10.1002/cpz1001.1084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Identification of N- and O-glycosylation on specific sites of proteins, along with glycan structural information, is necessary to determine the roles glycoproteins play in normal and pathologic cellular functions. Because such glycosylation is macro- and micro-heterogeneous and alters the dissociation behavior of glycopeptides, specific sample preparation, mass spectrometry, and data analysis techniques are required. Advanced tandem mass spectrometry-based glycoproteomics coupled with powerful data mining algorithms are key elements for characterization of protein glycosylation. This article includes the detailed, streamlined sample preparation method for liquid chromatography-mass spectrometry data acquisition and subsequent bioinformatics-based data annotation using the publicly available GlycReSoft program for highly efficient identification and quantification of glycoprotein glycosylation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Characterization of glycans and site occupancy on purified glycoprotein Support Protocol 1: In-gel digestion of glycoproteins Support Protocol 2: Detection of glycoproteins from cells/tissue through glycopeptide enrichment Basic Protocol 2: Acquisition of glycopeptides through high-resolution nano-LC-MS/MS Basic Protocol 3: Identification and quantification of glycopeptides using GlycReSoft.
Collapse
Affiliation(s)
- Meizhe Wang
- Department of Biochemistry, Boston University, Boston, Massachusetts
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Lauren E Pepi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Joseph Zaia
- Department of Biochemistry, Boston University, Boston, Massachusetts
- Bioinformatics Program, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts
| |
Collapse
|
22
|
Lee CCD, Watanabe Y, Wu NC, Han J, Kumar S, Pholcharee T, Seabright GE, Allen JD, Lin CW, Yang JR, Liu MT, Wu CY, Ward AB, Crispin M, Wilson IA. A cross-neutralizing antibody between HIV-1 and influenza virus. PLoS Pathog 2021; 17:e1009407. [PMID: 33750987 PMCID: PMC8016226 DOI: 10.1371/journal.ppat.1009407] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/01/2021] [Accepted: 02/17/2021] [Indexed: 11/19/2022] Open
Abstract
Incessant antigenic evolution enables the persistence and spread of influenza virus in the human population. As the principal target of the immune response, the hemagglutinin (HA) surface antigen on influenza viruses continuously acquires and replaces N-linked glycosylation sites to shield immunogenic protein epitopes using host-derived glycans. Anti-glycan antibodies, such as 2G12, target the HIV-1 envelope protein (Env), which is even more extensively glycosylated and contains under-processed oligomannose-type clusters on its dense glycan shield. Here, we illustrate that 2G12 can also neutralize human seasonal influenza A H3N2 viruses that have evolved to present similar oligomannose-type clusters on their HAs from around 20 years after the 1968 pandemic. Using structural biology and mass spectrometric approaches, we find that two N-glycosylation sites close to the receptor binding site (RBS) on influenza hemagglutinin represent the oligomannose cluster recognized by 2G12. One of these glycan sites is highly conserved in all human H3N2 strains and the other emerged during virus evolution. These two N-glycosylation sites have also become crucial for fitness of recent H3N2 strains. These findings shed light on the evolution of the glycan shield on influenza virus and suggest 2G12-like antibodies can potentially act as broad neutralizers to target human enveloped viruses.
Collapse
Affiliation(s)
- Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, England, United Kingdom
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, England, United Kingdom
| | - Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tossapol Pholcharee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gemma E. Seabright
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, England, United Kingdom
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Chih-Wei Lin
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ji-Rong Yang
- Centers for Disease Control, Taipei City, Taiwan
| | | | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| |
Collapse
|
23
|
Roberts DS, Mann MW, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33688648 DOI: 10.1101/2021.02.28.433291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.
Collapse
|
24
|
Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
Collapse
Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
Hackett WE, Zaia J. Calculating Glycoprotein Similarities From Mass Spectrometric Data. Mol Cell Proteomics 2021; 20:100028. [PMID: 32883803 PMCID: PMC8724611 DOI: 10.1074/mcp.r120.002223] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/24/2020] [Accepted: 09/03/2020] [Indexed: 12/23/2022] Open
Abstract
Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function. Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature. Quite often, however, the assumption behind proteomics that posttranslational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation. Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system. To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established. But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes. The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities. In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem.
Collapse
Affiliation(s)
- William E Hackett
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University, Boston, Massachusetts, USA.
| |
Collapse
|
27
|
Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
Collapse
Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
| |
Collapse
|
28
|
Schulze S, Oltmanns A, Fufezan C, Krägenbring J, Mormann M, Pohlschröder M, Hippler M. SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides. Bioinformatics 2020; 36:5330-5336. [PMID: 33325487 DOI: 10.1093/bioinformatics/btaa1042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Protein glycosylation is a complex post-translational modification with crucial cellular functions in all domains of life. Currently, large-scale glycoproteomics approaches rely on glycan database dependent algorithms and are thus unsuitable for discovery-driven analyses of glycoproteomes. RESULTS Therefore, we devised SugarPy, a glycan database independent Python module, and validated it on the glycoproteome of human breast milk. We further demonstrated its applicability by analyzing glycoproteomes with uncommon glycans stemming from the green alga Chlamydomonas reinhardtii and the archaeon Haloferax volcanii. SugarPy also facilitated the novel characterization of glycoproteins from the red alga Cyanidioschyzon merolae. AVAILABILITY The source code is freely available on GitHub (https://github.com/SugarPy/SugarPy), and its implementation in Python ensures support for all operating systems. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Stefan Schulze
- University of Pennsylvania, Department of Biology, Leidy Laboratories, Philadelphia, USA.,University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany
| | - Anne Oltmanns
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany
| | - Christian Fufezan
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Heidelberg, Germany
| | - Julia Krägenbring
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,University of Muenster, Institute for Hygiene, Muenster, Germany
| | - Michael Mormann
- University of Muenster, Institute for Hygiene, Muenster, Germany
| | - Mechthild Pohlschröder
- University of Pennsylvania, Department of Biology, Leidy Laboratories, Philadelphia, USA
| | - Michael Hippler
- University of Muenster, Institute of Plant Biology and Biotechnology, Muenster, Germany.,Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| |
Collapse
|
29
|
Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer. Nat Commun 2020; 11:6139. [PMID: 33262351 PMCID: PMC7708455 DOI: 10.1038/s41467-020-19976-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Inter-tumor heterogeneity is a result of genomic, transcriptional, translational, and post-translational molecular features. To investigate the roles of protein glycosylation in the heterogeneity of high-grade serous ovarian carcinoma (HGSC), we perform mass spectrometry-based glycoproteomic characterization of 119 TCGA HGSC tissues. Cluster analysis of intact glycoproteomic profiles delineates 3 major tumor clusters and 5 groups of intact glycopeptides. It also shows a strong relationship between N-glycan structures and tumor molecular subtypes, one example of which being the association of fucosylation with mesenchymal subtype. Further survival analysis reveals that intact glycopeptide signatures of mesenchymal subtype are associated with a poor clinical outcome of HGSC. In addition, we study the expression of mRNAs, proteins, glycosites, and intact glycopeptides, as well as the expression levels of glycosylation enzymes involved in glycoprotein biosynthesis pathways in each tumor. The results show that glycoprotein levels are mainly controlled by the expression of their individual proteins, and, furthermore, that the glycoprotein-modifying glycans correspond to the protein levels of glycosylation enzymes. The variation in glycan types further shows coordination to the tumor heterogeneity. Deeper understanding of the glycosylation process and glycosylation production in different subtypes of HGSC may provide important clues for precision medicine and tumor-targeted therapy. Altered protein glycosylation is increasingly recognized as a hallmark of cancer. Here, the authors profile the glycoproteome of 119 high-grade serous ovarian carcinoma tissues, showing that glycosylation patterns correlate with tumor molecular subtypes and clinical outcomes.
Collapse
|
30
|
White MR, Hsieh IN, De Luna X, Hartshorn KL. Effects of serum amyloid protein A on influenza A virus replication and viral interactions with neutrophils. J Leukoc Biol 2020; 110:155-166. [PMID: 33205458 PMCID: PMC7753654 DOI: 10.1002/jlb.4ab0220-116rr] [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: 03/24/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 01/22/2023] Open
Abstract
Innate immunity is vital for the early control of influenza A virus (IAV) infection. Serum amyloid A (SAA1) is an acute phase reactant produced in the liver and lung that rises dramatically during IAV infection. The potential role of SAA1 in host defense against IAV is unknown. SAA1 has been reported to directly activate neutrophils and to recruit them to the lung during infectious and inflammatory processes. Neutrophils are the most abundant cell recruited to the lung in the early phase of IAV infection. There are different forms and preparations of SAA1 that have found to have different effects on phagocyte responses, through various receptors. In this paper, we test the direct effects of various preparations of serum derived or recombinant SAA on IAV and how it modulates the interactions of IAV with neutrophils. All SAA preparations bound to IAV in vitro but caused minimal hemagglutination inhibition or viral aggregation. The human serum‐derived SAA1 or the complex of SAA1 with HDL did have IAV neutralizing activity in vitro, whereas the recombinant SAA1 preparations did not. We found that different SAA preparations also had markedly different effects on neutrophil functions, with E. coli‐derived SAA1 triggering some responses in neutrophils on its own or in presence of IAV whereas mammalian cell‐derived SAA1 did not. This discrepancy could be explained by the reported contamination of the former preparation with bacterial components. Of interest, however, serum SAA alone, serum SAA complexed with HDL, or HDL alone potentiated some neutrophil responses to IAV. Our results suggest that SAA may play some role in host response to IAV, but further work needs to be done to clarify the role of different variants of SAA alone or complexed with HDL.
Collapse
Affiliation(s)
- Mitchell R White
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - I-Ni Hsieh
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xavier De Luna
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Kevan L Hartshorn
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
31
|
Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J 2020; 119:2275-2289. [PMID: 33130120 DOI: 10.1016/j.bpj.2020.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/08/2020] [Accepted: 10/21/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase and are generally considered to inhibit antibody binding via their glycan shield. In this work, we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eightfold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e., the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase.
Collapse
|
32
|
Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
Collapse
Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
| |
Collapse
|
33
|
Hartshorn KL. Innate Immunity and Influenza A Virus Pathogenesis: Lessons for COVID-19. Front Cell Infect Microbiol 2020; 10:563850. [PMID: 33194802 PMCID: PMC7642997 DOI: 10.3389/fcimb.2020.563850] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
There is abundant evidence that the innate immune response to influenza A virus (IAV) is highly complex and plays a key role in protection against IAV induced infection and illness. Unfortunately it also clear that aspects of innate immunity can lead to severe morbidity or mortality from IAV, including inflammatory lung injury, bacterial superinfection, and exacerbation of reactive airways disease. We review broadly the virus and host factors that result in adverse outcomes from IAV and show evidence that inflammatory responses can become damaging even apart from changes in viral replication per se, with special focus on the positive and adverse effects of neutrophils and monocytes. We then evaluate in detail the role of soluble innate inhibitors including surfactant protein D and antimicrobial peptides that have a potential dual capacity for down-regulating viral replication and also inhibiting excessive inflammatory responses and how these innate host factors could possibly be harnessed to treat IAV infection. Where appropriate we draw comparisons and contrasts the SARS-CoV viruses and IAV in an effort to point out where the extensive knowledge existing regarding severe IAV infection could help guide research into severe COVID 19 illness or vice versa.
Collapse
Affiliation(s)
- Kevan L Hartshorn
- Section of Hematology Oncology, Boston University School of Medicine, Boston, MA, United States
| |
Collapse
|
34
|
Hu Y, Pan J, Shah P, Ao M, Thomas SN, Liu Y, Chen L, Schnaubelt M, Clark DJ, Rodriguez H, Boja ES, Hiltke T, Kinsinger CR, Rodland KD, Li QK, Qian J, Zhang Z, Chan DW, Zhang H. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma. Cell Rep 2020; 33:108276. [PMID: 33086064 PMCID: PMC7970828 DOI: 10.1016/j.celrep.2020.108276] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potential roles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.
Collapse
Affiliation(s)
- Yingwei Hu
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Jianbo Pan
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Stefani N Thomas
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.
| |
Collapse
|
35
|
Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Sci Rep 2020; 10:14991. [PMID: 32929138 PMCID: PMC7490396 DOI: 10.1038/s41598-020-71748-7] [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: 04/29/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the innate and adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight of the S trimer (17% for the HEK293 glycoform) they shield approximately 40% of the protein surface.
Collapse
Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
| |
Collapse
|
36
|
Chang D, Hackett WE, Zhong L, Wan XF, Zaia J. Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. Mol Cell Proteomics 2020; 19:1533-1545. [PMID: 32601173 PMCID: PMC8143645 DOI: 10.1074/mcp.ra120.002031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between WT IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though no N-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.
Collapse
Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William E Hackett
- Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Lei Zhong
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA; MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, Missouri, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA; Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA; Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA; MU Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA; Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
| |
Collapse
|
37
|
Hiono T, Kuno A. C-Terminally tagged NA in replication-competent influenza A viruses reveals differences in glycan profiles between NA and HA. Analyst 2020; 145:5845-5853. [PMID: 32830838 DOI: 10.1039/d0an00770f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycans attached to the viruses regulate their pathogenicity, immunogenicity, and antigenicity. We have previously shown that lectin microarray provided an easy and highly sensitive platform for analyzing glycan profiles of hemagglutinin (HA) of influenza A viruses in culture supernatants. On the other hand, the system is not applicable for neuraminidase (NA), the other viral glycoprotein of influenza A viruses, due to the limited availability of specific antibodies used to detect NA in the lectin microarray. Accordingly, we established replication-competent viruses harboring the short peptide-tag sequence at the C-terminus of NA in this study. The generated viruses underwent normal proliferation cycles and showed similar properties to the wild-type viruses. Lectin microarray analyses of the tagged NA enriched from the viral particles showed that glycan profiles of NA were mostly occupied by mannose-type glycans. Interestingly, the profiles were distinct from those of HA separated from the same particle preparation, in which core-fucosylated complex-type N-glycans terminating with non-sialylated N-acetyllactosamine were dominant. Collectively, this study provides novel platforms for the analyses of the distinction between the glycan profiles of NA and HA, and contributes to a better understanding of later stages of the viral life cycles through analyzing the glycans attached to NA.
Collapse
Affiliation(s)
- Takahiro Hiono
- Molecular & Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan.
| | | |
Collapse
|
38
|
Khodadadi E, Zeinalzadeh E, Taghizadeh S, Mehramouz B, Kamounah FS, Khodadadi E, Ganbarov K, Yousefi B, Bastami M, Kafil HS. Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies. Infect Drug Resist 2020; 13:1785-1806. [PMID: 32606829 PMCID: PMC7305820 DOI: 10.2147/idr.s238446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.
Collapse
Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
39
|
Thompson AJ, Cao L, Ma Y, Wang X, Diedrich JK, Kikuchi C, Willis S, Worth C, McBride R, Yates JR, Paulson JC. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe 2020; 27:725-735.e5. [PMID: 32298658 PMCID: PMC7158820 DOI: 10.1016/j.chom.2020.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/13/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hemagglutinins (HAs) from human influenza viruses adapt to bind α2-6-linked sialosides, overcoming a receptor-defined species barrier distinct from the α2-3 specificity of avian virus progenitors. Additionally, human-adapted HAs gain glycosylation sites over time, although their biological function is poorly defined. Using quantitative glycomic analysis, we show that HAs from human pandemic viruses exhibit significant proportions of high-mannose type N-linked glycans throughout the head domain. By contrast, poorly adapted avian-origin HAs contain predominately complex-type glycans, which have greater structural diversity. Although oligomannose levels vary, they are present in all tested recombinant HAs and whole viruses and can be specifically targeted for universal detection. The positions of high-mannose glycosites on the HA of human H1N1 and H3N2 strains are conserved. Additionally, high-mannose-binding lectins possess a broad capacity to neutralize and prevent infection with contemporary H3N2 strains. These findings reveal the biological significance of HA glycosylation and therapeutic potential of targeting these structures.
Collapse
Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Liwei Cao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Chika Kikuchi
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shelby Willis
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Charli Worth
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, Scripps Research, La Jolla, CA 92037, USA.
| |
Collapse
|
40
|
Li L, Chang D, Han L, Zhang X, Zaia J, Wan XF. Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin. BMC Bioinformatics 2020; 21:182. [PMID: 32393178 PMCID: PMC7216668 DOI: 10.1186/s12859-020-3527-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determined by both protein sequence and N-linked glycosylation of influenza glycoproteins, especially hemagglutinin (HA). The currently available computational methods are only considered features in protein sequence but not N-linked glycosylation. RESULTS A multi-task learning sparse group least absolute shrinkage and selection operator (LASSO) (MTL-SGL) regression method was developed and applied to derive two types of predominant features including protein sequence and N-linked glycosylation in hemagglutinin (HA) affecting variations in serologic data for human and swine H1N1 IAVs. Results suggested that mutations and changes in N-linked glycosylation sites are associated with the rise of antigenic variants of H1N1 IAVs. Furthermore, the implicated mutations are predominantly located at five reported antibody-binding sites, and within or close to the HA receptor binding site. All of the three N-linked glycosylation sites (i.e. sequons NCSV at HA 54, NHTV at HA 125, and NLSK at HA 160) identified by MTL-SGL to determine antigenic changes were experimentally validated in the H1N1 antigenic variants using mass spectrometry analyses. Compared with conventional sparse learning methods, MTL-SGL achieved a lower prediction error and higher accuracy, indicating that grouped features and MTL in the MTL-SGL method are not only able to handle serologic data generated from multiple reagents, supplies, and protocols, but also perform better in genetic sequence-based antigenic quantification. CONCLUSIONS In summary, the results of this study suggest that mutations and variations in N-glycosylation in HA caused antigenic variations in H1N1 IAVs and that the sequence-based antigenicity predictive model will be useful in understanding antigenic evolution of IAVs.
Collapse
Affiliation(s)
- Lei Li
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Deborah Chang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.,Tencent AI Lab, Shenzhen, China
| | - Xiaojian Zhang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.,MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA. .,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA. .,MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, MO, USA. .,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA. .,MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
41
|
Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.07.030445. [PMID: 32511307 PMCID: PMC7217288 DOI: 10.1101/2020.04.07.030445] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight (17% for the HEK293 glycoform) the level of surface shielding is disproportionately high at 42%.
Collapse
Affiliation(s)
- Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| |
Collapse
|
42
|
The OAAH Family: Anti-Influenza Virus Lectins. Methods Mol Biol 2020. [PMID: 32306367 DOI: 10.1007/978-1-0716-0430-4_59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
High mannose (HM)-binding Oscillatoria agardhii agglutinin homologue (OAAH) lectin family is an important class of anti-viral proteins. The OAAH family lectins show potent anti-influenza virus activity with EC50 of nanomolar levels by binding to HM glycans of the envelope glycoprotein hemagglutinin (HA), thereby inhibiting the viral entry into host cells. No broadly effective neutralizing vaccines for influenza virus are available due to the frequent antigenic drift caused by rapid mutations. Alternatives for vaccines need to be developed to prepare for a possible risk of future emergence of a highly virulent virus. Possible use of antiviral lectins is a simple and useful strategy to prevent viral infection by interfering with the interaction between viral HA and the host sialic acid-containing receptor. High-density glycans of surface HA are primary targets for the lectins to inhibit viral entry. In general, the anti-influenza virus potency of lectins is evaluated by a series of inhibitory assays for infection, such as neutral red dye uptake assay to determine the extent of viral cytopathic effect, and immunofluorescence microscopy to detect the expression of viral proteins in infected cells. Direct interaction between lectins and HA could be evaluated by enzyme-linked immunosorbent assay or surface plasmon resonance analysis.
Collapse
|
43
|
Klein J, Zaia J. Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS. J Proteome Res 2020; 19:2113-2121. [PMID: 32223173 DOI: 10.1021/acs.jproteome.0c00051] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glycopeptides identified by tandem mass spectrometry rely on the identification of the peptide backbone sequence and the attached glycan(s) by the incomplete fragmentation of both moieties. This may lead to ambiguous identifications where multiple structures could explain the same spectrum equally well due to missing information in the mass spectrum or incorrect precursor mass determination. To date, approaches to solving these problems have been limited, and few inroads have been made to address these issues. We present a technique to address some of these challenges and demonstrate it on previously published data sets. We use a linear modeling approach to learn the influence of the glycan composition on the retention time of a glycopeptide and use these models to validate glycopeptides within the same experiment, detecting over 400 incorrect cases during the MS/MS search and correcting 75 cases that could not be identified based on mass alone. We make this technique available as a command line executable program, written in Python and C, freely available at https://github.com/mobiusklein/glycresoft in source form, with precompiled binaries for Windows.
Collapse
Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States.,Department of Biochemistry, Boston University, Boston, Massachusetts 02215, United States
| |
Collapse
|
44
|
Influenza Virus Hemagglutinins H2, H5, H6, and H11 Are Not Targets of Pulmonary Surfactant Protein D: N-Glycan Subtypes in Host-Pathogen Interactions. J Virol 2020; 94:JVI.01951-19. [PMID: 31826991 DOI: 10.1128/jvi.01951-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/01/2019] [Indexed: 11/20/2022] Open
Abstract
Seasonal influenza carrying key hemagglutinin (HA) head region glycosylation sites can be removed from the lung by pulmonary surfactant protein D (SP-D). Little is known about HA head glycosylation of low-pathogenicity avian influenza virus (LPAIV) subtypes. These can pose a pandemic threat through reassortment and emergence in human populations. Since the presence of head region high-mannose glycosites dictates SP-D activity, the ability to predict these glycosite glycan subtypes may be of value. Here, we investigate the activities of two recombinant human SP-D forms against representative LPAIV strains, including H2N1, H5N1, H6N1, H11N9, an avian H3N8, and a human seasonal H3N2 subtype. Using mass spectrometry, we determined the glycan subclasses and heterogeneities at each head glycosylation site. Sequence alignment and molecular structure analysis of the HAs were performed for LPAIV strains in comparison to seasonal H3N2 and avian H3N8. Intramolecular contacts were determined between the protein backbone and glycosite glycan based on available three-dimensional structure data. We found that glycosite "N165" (H3 numbering) is occupied by high-mannose glycans in H3 HA but by complex glycans in all LPAIV HAs. SP-D was not active on LPAIV but was on H3 HAs. Since SP-D affinity for influenza HA depends on the presence of high-mannose glycan on the head region, our data demonstrate that SP-D may not protect against virus containing these HA subtypes. Our results also demonstrate that glycan subtype can be predicted at some glycosites based on sequence comparisons and three-dimensional structural analysis.IMPORTANCE Low-pathogenicity avian influenza virus (LPAIV) subtypes can reassort with circulating human strains and pandemic viruses can emerge in human populations, as was seen in the 1957 pandemic, in which an H2 virus reassorted with the circulating H1N1 to create a novel H2N2 genotype. Lung surfactant protein D (SP-D), a key factor in first-line innate immunity defense, removes influenza type A virus (IAV) through interaction with hemagglutinin (HA) head region high-mannose glycan(s). While it is known that both H1 and H3 HAs have one or more key high-mannose glycosites in the head region, little is known about similar glycosylation of LPAIV strains H2N1, H5N1, H6N1, or H11N9, which may pose future health risks. Here, we demonstrate that the hemagglutinins of LPAIV strains do not have the required high-mannose glycans and do not interact with SP-D, and that sequence analysis can predict glycan subtype, thus predicting the presence or absence of this virulence marker.
Collapse
|
45
|
|
46
|
Ateia M, Alalm MG, Awfa D, Johnson MS, Yoshimura C. Modeling the degradation and disinfection of water pollutants by photocatalysts and composites: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134197. [PMID: 31494425 DOI: 10.1016/j.scitotenv.2019.134197] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/20/2019] [Accepted: 08/29/2019] [Indexed: 05/26/2023]
Abstract
Recently, a series of new photocatalysts have been developed for to combat diverse bio-recalcitrant contaminants and the inactivation of bacteria. Modeling photocatalytic processes is important to assess these materials, and to understand and optimize their performance. In this study, the recent literature is critically reviewed and analyzed to identify and compare methods of modeling photocatalytic performance. The Langmuir-Hinshelwood model (L-H) has been used in many studies to rationalize the degradation kinetics of single contaminants because it is the simplest model including both the adsorption equilibrium and degradation rates. Other studies report the development of more sophisticated variants of the L-H model that include the rates of catalyst excitation, recombination of electron-hole pairs, production of reactive oxygen species (ROS), and formation of by-products. Modified Chick-Watson (CW) and Hom models have been used by many researchers to include lag phases of bacteria in the description of disinfection kinetics. Artificial neural networks (ANNs) have been used to analyze the effects of operational conditions on photocatalyst performance. Moreover, response surface methodology (RSM) has been employed for experimental design, and optimization of operational conditions. We have reviewed and analyzed all available articles that model photocatalytic activity towards water pollution, summarized and put them in context, and recommended future research directions.
Collapse
Affiliation(s)
- Mohamed Ateia
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, United States.
| | - Mohamed Gar Alalm
- Department of Public Works Engineering, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt.
| | - Dion Awfa
- Department of Civil and Environmental Engineering, School of Environment and Society, Tokyo Institute of Technology, 2-12-1, M1-4, Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Matthew S Johnson
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Chihiro Yoshimura
- Department of Civil and Environmental Engineering, School of Environment and Society, Tokyo Institute of Technology, 2-12-1, M1-4, Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| |
Collapse
|
47
|
Chang D, Zaia J. Why Glycosylation Matters in Building a Better Flu Vaccine. Mol Cell Proteomics 2019; 18:2348-2358. [PMID: 31604803 PMCID: PMC6885707 DOI: 10.1074/mcp.r119.001491] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/18/2019] [Indexed: 12/20/2022] Open
Abstract
Low vaccine efficacy against seasonal influenza A virus (IAV) stems from the ability of the virus to evade existing immunity while maintaining fitness. Although most potent neutralizing antibodies bind antigenic sites on the globular head domain of the IAV envelope glycoprotein hemagglutinin (HA), the error-prone IAV polymerase enables rapid evolution of key antigenic sites, resulting in immune escape. Significantly, the appearance of new N-glycosylation consensus sequences (sequons, NXT/NXS, rarely NXC) on the HA globular domain occurs among the more prevalent mutations as an IAV strain undergoes antigenic drift. The appearance of new glycosylation shields underlying amino acid residues from antibody contact, tunes receptor specificity, and balances receptor avidity with virion escape, all of which help maintain viral propagation through seasonal mutations. The World Health Organization selects seasonal vaccine strains based on information from surveillance, laboratory, and clinical observations. Although the genetic sequences are known, mature glycosylated structures of circulating strains are not defined. In this review, we summarize mass spectrometric methods for quantifying site-specific glycosylation in IAV strains and compare the evolution of IAV glycosylation to that of human immunodeficiency virus. We argue that the determination of site-specific glycosylation of IAV glycoproteins would enable development of vaccines that take advantage of glycosylation-dependent mechanisms whereby virus glycoproteins are processed by antigen presenting cells.
Collapse
Affiliation(s)
- Deborah Chang
- Dept. of Biochemistry, Boston University School of Medicine, Boston, MA 02118
| | - Joseph Zaia
- Dept. of Biochemistry, Boston University School of Medicine, Boston, MA 02118.
| |
Collapse
|
48
|
Klein J, Carvalho L, Zaia J. Application of network smoothing to glycan LC-MS profiling. Bioinformatics 2019; 34:3511-3518. [PMID: 29790907 DOI: 10.1093/bioinformatics/bty397] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/10/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting. Existing tools for interpreting the resulting data do not take into account related glycans when evaluating individual observations, limiting their sensitivity. Results We developed an algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans. Our algorithm optimizes a set of likelihood scoring functions based on glycan chemical properties but uses network Laplacian regularization and optionally prior information about expected glycan families to smooth the likelihood and thus achieve a consistent and more representative solution. Our method was able to identify as many, or more glycan compositions compared to previous approaches, and demonstrated greater sensitivity with regularization. Our network definition was tailored to N-glycans but the method may be applied to glycomics data from other glycan families like O-glycans or heparan sulfate where the relationships between compositions can be expressed as a graph. Availability and implementation Built Executable http://www.bumc.bu.edu/msr/glycresoft/ and Source Code: https://github.com/BostonUniversityCBMS/glycresoft. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, MA, USA
| | - Luis Carvalho
- Program for Bioinformatics, Boston University, Boston, MA, USA.,Department of Math and Statistics, Boston University, Boston, MA, USA
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, MA, USA.,Department of Biochemistry, Boston University, Boston, MA, USA
| |
Collapse
|
49
|
Raghunathan R, Sethi MK, Zaia J. On-slide tissue digestion for mass spectrometry based glycomic and proteomic profiling. MethodsX 2019; 6:2329-2347. [PMID: 31660297 PMCID: PMC6807300 DOI: 10.1016/j.mex.2019.09.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
We describe a protocol for glycomic and proteomic profiling that uses serial enzyme digestions from the surface of fresh frozen or fixed tissue slides. The abundances of the extracted glycans and peptides are determined using liquid chromatography-mass spectrometry. In a typical experiment, our method quantifies 14 heparan sulfate disaccharides, 11 chondroitin sulfate disaccharides, 50 N-glycan compositions and approximately 1200 proteins from a 1.8 mm circle, on the surface of a fresh frozen tissue slide from rat brain. Each enzymatic digestion is incubated overnight with direct application of enzyme on the tissue surface. Overall, the sample preparation process for multiple tissue slides takes a day per biomolecule class. This protocol saves time by simultaneous digestion of large N-glycans and small HS disaccharides and subsequent separation using size exclusion chromatography. Compared to wet tissue analysis, this method requires less time by a factor of two. By comparison, MALDI-imaging provides higher spatial resolution of glycans and proteins but lower depth of coverage. MALDI dissociates fragile glycan substituents including sulfates and is not recommended for analysis of glycosaminoglycans (GAGs).
Collapse
Affiliation(s)
- Rekha Raghunathan
- Boston University, Molecular and Translational Medicine, Boston, 02118, USA
| | - Manveen K Sethi
- Boston University, Dept. of Biochemistry, Boston, 02118, USA
| | - Joseph Zaia
- Boston University, Molecular and Translational Medicine, Boston, 02118, USA.,Boston University, Dept. of Biochemistry, Boston, 02118, USA
| |
Collapse
|
50
|
Unione L, Lenza M, Ardá A, Urquiza P, Laín A, Falcón-Pérez JM, Jiménez-Barbero J, Millet O. Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy. ACS CENTRAL SCIENCE 2019; 5:1554-1561. [PMID: 31572782 PMCID: PMC6764210 DOI: 10.1021/acscentsci.9b00540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 05/10/2023]
Abstract
Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.
Collapse
Affiliation(s)
- Luca Unione
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
| | - Maria
Pia Lenza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Pedro Urquiza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Laín
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Juan Manuel Falcón-Pérez
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
- Dept.
Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- E-mail:
| | - Oscar Millet
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
| |
Collapse
|