1
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Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024; 49:916-931. [PMID: 39054240 PMCID: PMC11455608 DOI: 10.1016/j.tibs.2024.06.012] [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: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
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Affiliation(s)
- Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Biological Structure Physics and Design Graduate Program, University of Washington, Seattle, WA, USA.
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2
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Badiee SA, Kumar VG, Moradi M. Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602399. [PMID: 39026831 PMCID: PMC11257422 DOI: 10.1101/2024.07.07.602399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (His106 2 ) located in the hinge region of HA2. Our analysis encompassed comparisons between non-protonated (NP), partially protonated (1P, 2P), and fully-protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the non-protonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully-protonated system (3P) compared to non-protonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.
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3
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [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: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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4
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Sänger L, Williams HM, Yu D, Vogel D, Kosinski J, Rosenthal M, Uetrecht C. RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment. J Am Chem Soc 2023; 145:27958-27974. [PMID: 38104324 PMCID: PMC10755698 DOI: 10.1021/jacs.3c07325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Lassa virus is a negative-strand RNA virus with only four structural proteins that causes periodic outbreaks in West Africa. The nucleoprotein (NP) encapsidates the viral genome, forming ribonucleoprotein complexes (RNPs) together with the viral RNA and the L protein. RNPs must be continuously restructured during viral genome replication and transcription. The Z protein is important for membrane recruitment of RNPs, viral particle assembly, and budding and has also been shown to interact with the L protein. However, the interaction of NP, viral RNA, and Z is poorly understood. Here, we characterize the interactions between Lassa virus NP, Z, and RNA using structural mass spectrometry. We identify the presence of RNA as the driver for the disassembly of ring-like NP trimers, a storage form, into monomers to subsequently form higher order RNA-bound NP assemblies. We locate the interaction site of Z and NP and demonstrate that while NP binds Z independently of the presence of RNA, this interaction is pH-dependent. These data improve our understanding of RNP assembly, recruitment, and release in Lassa virus.
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Affiliation(s)
- Lennart Sänger
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Harry M. Williams
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
| | - Dingquan Yu
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
| | - Dominik Vogel
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Jan Kosinski
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Maria Rosenthal
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
- Faculty
V: School of Life Sciences, University of
Siegen, Am Eichenhang 50, 57076 Siegen, Germany
- Deutsches
Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
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5
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David SC, Vadas O, Glas I, Schaub A, Luo B, D'angelo G, Montoya JP, Bluvshtein N, Hugentobler W, Klein LK, Motos G, Pohl M, Violaki K, Nenes A, Krieger UK, Stertz S, Peter T, Kohn T. Inactivation mechanisms of influenza A virus under pH conditions encountered in aerosol particles as revealed by whole-virus HDX-MS. mSphere 2023; 8:e0022623. [PMID: 37594288 PMCID: PMC10597348 DOI: 10.1128/msphere.00226-23] [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: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/19/2023] Open
Abstract
Multiple respiratory viruses, including influenza A virus (IAV), can be transmitted via expiratory aerosol particles, and aerosol pH was recently identified as a major factor influencing airborne virus infectivity. Indoors, small exhaled aerosols undergo rapid acidification to pH ~4. IAV is known to be sensitive to mildly acidic conditions encountered within host endosomes; however, it is unknown whether the same mechanisms could mediate viral inactivation within the more acidic aerosol micro-environment. Here, we identified that transient exposure to pH 4 caused IAV inactivation by a two-stage process, with an initial sharp decline in infectious titers mainly attributed to premature attainment of the post-fusion conformation of viral protein haemagglutinin (HA). Protein changes were observed by hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) as early as 10 s post-exposure to acidic conditions. Our HDX-MS data are in agreement with other more labor-intensive structural analysis techniques, such as X-ray crystallography, highlighting the ease and usefulness of whole-virus HDX-MS for multiplexed protein analyses, even within enveloped viruses such as IAV. Additionally, virion integrity was partially but irreversibly affected by acidic conditions, with a progressive unfolding of the internal matrix protein 1 (M1) that aligned with a more gradual decline in viral infectivity with time. In contrast, no acid-mediated changes to the genome or lipid envelope were detected. Improved understanding of respiratory virus fate within exhaled aerosols constitutes a global public health priority, and information gained here could aid the development of novel strategies to control the airborne persistence of seasonal and/or pandemic influenza in the future. IMPORTANCE It is well established that COVID-19, influenza, and many other respiratory diseases can be transmitted by the inhalation of aerosolized viruses. Many studies have shown that the survival time of these airborne viruses is limited, but it remains an open question as to what drives their infectivity loss. Here, we address this question for influenza A virus by investigating structural protein changes incurred by the virus under conditions relevant to respiratory aerosol particles. From prior work, we know that expelled aerosols can become highly acidic due to equilibration with indoor room air, and our results indicate that two viral proteins are affected by these acidic conditions at multiple sites, leading to virus inactivation. Our findings suggest that the development of air treatments to quicken the speed of aerosol acidification would be a major strategy to control infectious bioburdens in the air.
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Affiliation(s)
- Shannon C. David
- Environmental Chemistry Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Oscar Vadas
- Protein Platform, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Aline Schaub
- Environmental Chemistry Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Beiping Luo
- Institute for Atmospheric and Climate Science, ETH Zurich, Zürich, Switzerland
| | - Giovanni D'angelo
- Laboratory of Lipid Cell Biology, School of Life Sciences, Interschool Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Paz Montoya
- Laboratory of Lipid Cell Biology, School of Life Sciences, Interschool Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nir Bluvshtein
- Institute for Atmospheric and Climate Science, ETH Zurich, Zürich, Switzerland
| | - Walter Hugentobler
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Liviana K. Klein
- Institute for Atmospheric and Climate Science, ETH Zurich, Zürich, Switzerland
| | - Ghislain Motos
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie Pohl
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Kalliopi Violaki
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Athanasios Nenes
- Laboratory of Atmospheric Processes and their Impacts, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas, Patras, Greece
| | - Ulrich K. Krieger
- Institute for Atmospheric and Climate Science, ETH Zurich, Zürich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climate Science, ETH Zurich, Zürich, Switzerland
| | - Tamar Kohn
- Environmental Chemistry Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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6
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Garcia NK, Kephart SM, Benhaim MA, Matsui T, Mileant A, Guttman M, Lee KK. Structural dynamics reveal subtype-specific activation and inhibition of influenza virus hemagglutinin. J Biol Chem 2023; 299:104765. [PMID: 37121546 PMCID: PMC10220487 DOI: 10.1016/j.jbc.2023.104765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/25/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023] Open
Abstract
Influenza hemagglutinin (HA) is a prototypical class 1 viral entry glycoprotein, responsible for mediating receptor binding and membrane fusion. Structures of its prefusion and postfusion forms, embodying the beginning and endpoints of the fusion pathway, have been extensively characterized. Studies probing HA dynamics during fusion have begun to identify intermediate states along the pathway, enhancing our understanding of how HA becomes activated and traverses its conformational pathway to complete fusion. HA is also the most variable, rapidly evolving part of influenza virus, and it is not known whether mechanisms of its activation and fusion are conserved across divergent viral subtypes. Here, we apply hydrogen-deuterium exchange mass spectrometry to compare fusion activation in two subtypes of HA, H1 and H3. Our data reveal subtype-specific behavior in the regions of HA that undergo structural rearrangement during fusion, including the fusion peptide and HA1/HA2 interface. In the presence of an antibody that inhibits the conformational change (FI6v3), we observe that acid-induced dynamic changes near the epitope are dampened, but the degree of protection at the fusion peptide is different for the two subtypes investigated. These results thus provide new insights into variation in the mechanisms of influenza HA's dynamic activation and its inhibition.
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Affiliation(s)
- Natalie K Garcia
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Mark A Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Laboratory, SLAC, Menlo Park, California, USA
| | - Alexander Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
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7
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Aganovic A. pH-dependent endocytosis mechanisms for influenza A and SARS-coronavirus. Front Microbiol 2023; 14:1190463. [PMID: 37234537 PMCID: PMC10206014 DOI: 10.3389/fmicb.2023.1190463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The ongoing SARS-CoV-2 pandemic and the influenza epidemics have revived the interest in understanding how these highly contagious enveloped viruses respond to alterations in the physicochemical properties of their microenvironment. By understanding the mechanisms and conditions by which viruses exploit the pH environment of the host cell during endocytosis, we can gain a better understanding of how they respond to pH-regulated anti-viral therapies but also pH-induced changes in extracellular environments. This review provides a detailed explanation of the pH-dependent viral structural changes preceding and initiating viral disassembly during endocytosis for influenza A (IAV) and SARS coronaviruses. Drawing upon extensive literature from the last few decades and latest research, I analyze and compare the circumstances in which IAV and SARS-coronavirus can undertake endocytotic pathways that are pH-dependent. While there are similarities in the pH-regulated patterns leading to fusion, the mechanisms and pH activation differ. In terms of fusion activity, the measured activation pH values for IAV, across all subtypes and species, vary between approximately 5.0 to 6.0, while SARS-coronavirus necessitates a lower pH of 6.0 or less. The main difference between the pH-dependent endocytic pathways is that the SARS-coronavirus, unlike IAV, require the presence of specific pH-sensitive enzymes (cathepsin L) during endosomal transport. Conversely, the conformational changes in the IAV virus under acidic conditions in endosomes occur due to the specific envelope glycoprotein residues and envelope protein ion channels (viroporins) getting protonated by H+ ions. Despite extensive research over several decades, comprehending the pH-triggered conformational alterations of viruses still poses a significant challenge. The precise mechanisms of protonation mechanisms of certain during endosomal transport for both viruses remain incompletely understood. In absence of evidence, further research is needed.
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Affiliation(s)
- Amar Aganovic
- Faculty of Engineering Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
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8
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Klein S, Golani G, Lolicato F, Lahr C, Beyer D, Herrmann A, Wachsmuth-Melm M, Reddmann N, Brecht R, Hosseinzadeh M, Kolovou A, Makroczyova J, Peterl S, Schorb M, Schwab Y, Brügger B, Nickel W, Schwarz US, Chlanda P. IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion. Cell Host Microbe 2023; 31:616-633.e20. [PMID: 37003257 DOI: 10.1016/j.chom.2023.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically affects virus fusion with target cell membranes. We found that IFITM3 induces local lipid sorting, resulting in an increased concentration of lipids disfavoring viral fusion at the hemifusion site. This increases the energy barrier for fusion pore formation and the hemifusion dwell time, promoting viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion. Observation of hemifusion diaphragms between viral particles and late endosomal membranes confirmed hemifusion stabilization as a molecular mechanism of IFITM3. The presence of the influenza fusion protein hemagglutinin in post-fusion conformation close to hemifusion sites further indicated that IFITM3 does not interfere with the viral fusion machinery. Collectively, these findings show that IFITM3 induces lipid sorting to stabilize hemifusion and prevent virus entry into target cells.
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Affiliation(s)
- Steffen Klein
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Gonen Golani
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland
| | - Carmen Lahr
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Daniel Beyer
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Alexia Herrmann
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Nina Reddmann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Romy Brecht
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mehdi Hosseinzadeh
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Androniki Kolovou
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Sarah Peterl
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Ulrich S Schwarz
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany.
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9
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Villamil Giraldo AM, Mannsverk S, Kasson PM. Measuring single-virus fusion kinetics using an assay for nucleic acid exposure. Biophys J 2022; 121:4467-4475. [PMID: 36330566 PMCID: PMC9748363 DOI: 10.1016/j.bpj.2022.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
The kinetics by which individual enveloped viruses fuse with membranes provide an important window into viral-entry mechanisms. We have developed a real-time assay using fluorescent probes for single-virus genome exposure than can report on stages of viral entry including or subsequent to fusion pore formation and prior to viral genome trafficking. We accomplish this using oxazole yellow nucleic-acid-binding dyes, which can be encapsulated in the lumen of target membranes to permit specific detection of fusion events. Since increased fluorescence of the dye occurs only when it encounters viral genome via a fusion pore and binds, this assay excludes content leakage without fusion. Using this assay, we show that influenza virus fuses with liposomes of different sizes with indistinguishable kinetics by both testing liposomes extruded through pores of different radii and showing that the fusion kinetics of individual liposomes are uncorrelated with the size of the liposome. These results suggest that the starting curvature of such liposomes does not control the rate-limiting steps in influenza entry.
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Affiliation(s)
- Ana M Villamil Giraldo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Steinar Mannsverk
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia.
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10
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Li Z, Li T, Liu M, Ivanovic T. Hemagglutinin Stability Determines Influenza A Virus Susceptibility to a Broad-Spectrum Fusion Inhibitor Arbidol. ACS Infect Dis 2022; 8:1543-1552. [PMID: 35819162 PMCID: PMC9810120 DOI: 10.1021/acsinfecdis.2c00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Understanding mechanisms of resistance to antiviral inhibitors can reveal nuanced features of targeted viral mechanisms and, in turn, lead to improved strategies for inhibitor design. Arbidol is a broad-spectrum antiviral that binds to and prevents the fusion-associated conformational changes in the trimeric influenza A virus (IAV) hemagglutinin (HA). The rate-limiting step during the HA-mediated membrane fusion is the release of the hydrophobic fusion peptides from a conserved pocket on HA. Here, we investigated how destabilizing or stabilizing mutations in or near the fusion peptide affect viral sensitivity to Arbidol. The degree of sensitivity was proportional to the extent of fusion-peptide stability on the prefusion HA: stabilized mutants were more sensitive, and destabilized ones were resistant to Arbidol. Single-virion membrane fusion experiments for representative wild-type (WT) and mutant viruses demonstrated that resistance is a direct consequence of fusion-peptide destabilization not requiring reduced Arbidol binding to HA. Our results support the model whereby the probability of individual HAs extending to engage the target membrane is determined by the composite of two critical forces: a "tug" on the fusion peptide by HA rearrangements near the Arbidol binding site and the key interactions stabilizing the fusion peptide in the prefusion pocket. Arbidol increases and destabilizing mutations decrease the free-energy cost for fusion-peptide release, accounting for the observed resistance. Our findings have broad implications for fusion inhibitor design, viral mechanisms of resistance, and our basic understanding of HA-mediated membrane fusion.
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11
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Trabjerg E, Keller A, Leitner A. pH Dependence of Succinimide-Ester-Based Protein Cross-Linking for Structural Mass Spectrometry Applications. ACS MEASUREMENT SCIENCE AU 2022; 2:132-138. [PMID: 36785722 PMCID: PMC9838815 DOI: 10.1021/acsmeasuresciau.1c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Within the research field of cross-linking mass spectrometry (XL-MS), the most commonly used cross-linking reagents are succinimide-ester-based (e.g., disuccinimidyl suberate (DSS)). These reagents primarily cross-link lysine side chains. So far, they have predominantly been used to investigate protein structures at neutral to slightly basic pH (7.0-8.5) to ensure the reactivity of the primary amine of the lysine side chain. However, disease-related molecular processes are not limited to such pH ranges; e.g., some important biological pathways are active in acidic intracellular compartments. The applicability of lysine-reactive cross-linking reagents to low-pH conditions remains unclear. Here, we cross-linked a mixture of eight model proteins at eight different pH conditions (pH 4.0-7.5) to investigate the pH dependency of DSS. DSS was able to cross-link proteins even at pH 4.0, but a clear decrease in the cross-linking efficiency was observed when the pH was lowered. Nevertheless, at pH 5.0, approximately half of the number of cross-links observed at pH 7.5 could still be identified. These findings highlight the ability of succinimide-based cross-linking reagents to be useful in probing the structure of proteins in a slightly acidic environment.
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12
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Huang QJ, Song K, Xu C, Bolon DNA, Wang JP, Finberg RW, Schiffer CA, Somasundaran M. Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks. Structure 2022; 30:777-786.e3. [PMID: 35290796 PMCID: PMC9610019 DOI: 10.1016/j.str.2022.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 02/17/2022] [Indexed: 01/01/2023]
Abstract
Influenza viruses pose severe public health threats globally. Influenza viruses are extensively pleomorphic, in shape, size, and organization of viral proteins. Analysis of influenza morphology and ultrastructure can help elucidate viral structure-function relationships and aid in therapeutics and vaccine development. While cryo-electron tomography (cryoET) can depict the 3D organization of pleomorphic influenza, the low signal-to-noise ratio inherent to cryoET and viral heterogeneity have precluded detailed characterization of influenza viruses. In this report, we leveraged convolutional neural networks and cryoET to characterize the morphological architecture of the A/Puerto Rico/8/34 (H1N1) influenza strain. Our pipeline improved the throughput of cryoET analysis and accurately identified viral components within tomograms. Using this approach, we successfully characterized influenza morphology, glycoprotein density, and conducted subtomogram averaging of influenza glycoproteins. Application of this processing pipeline can aid in the structural characterization of not only influenza viruses, but other pleomorphic viruses and infected cells.
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Affiliation(s)
- Qiuyu J Huang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kangkang Song
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Jennifer P Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Robert W Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
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13
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Kovalevskiy SA, Lopatina OA, Gushchina EA, Isaeva EI, Fedyakina IT, Baklanova OV, Mezentseva MV, Balashov EM, Ivashkevich NM, Kulak AI, Dalidchik FI. Destruction of the Shell of Influenza Viruses by Heteropoly Acids with Keggin Structure. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121060051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Caffrey M, Lavie A. pH-Dependent Mechanisms of Influenza Infection Mediated by Hemagglutinin. Front Mol Biosci 2022; 8:777095. [PMID: 34977156 PMCID: PMC8718792 DOI: 10.3389/fmolb.2021.777095] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza hemagglutinin (HA) is a viral membrane bound protein that plays a critical role in the viral life cycle by mediating entry into target cells. HA exploits the lowering of the pH in the endosomal compartment to initiate a series of conformational changes that promote access of the viral genetic material to the cytoplasm, and hence viral replication. In this review we will first discuss what is known about the structural properties of HA as a function of pH. Next, we will discuss the dynamics and intermediate states of HA. We will then discuss the specific residues that are thought to be titrated by the change in pH and possible mechanisms for the pH triggered conformational changes. Finally, we will discuss small molecules that disrupt the pH trigger and thus serve as potential therapeutic strategies to prevent influenza infection.
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Affiliation(s)
- Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States
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15
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Muñoz-Moreno R, Martínez-Romero C, García-Sastre A. Induction and Evasion of Type-I Interferon Responses during Influenza A Virus Infection. Cold Spring Harb Perspect Med 2021; 11:a038414. [PMID: 32661015 PMCID: PMC8485741 DOI: 10.1101/cshperspect.a038414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Influenza A viruses (IAVs) are contagious pathogens and one of the leading causes of respiratory tract infections in both humans and animals worldwide. Upon infection, the innate immune system provides the first line of defense to neutralize or limit the replication of invading pathogens, creating a fast and broad response that brings the cells into an alerted state through the secretion of cytokines and the induction of the interferon (IFN) pathway. At the same time, IAVs have developed a plethora of immune evasion mechanisms in order to avoid or circumvent the host antiviral response, promoting viral replication. Herein, we will review and summarize already known and recently described innate immune mechanisms that host cells use to fight IAV viral infections as well as the main strategies developed by IAVs to overcome such powerful defenses during this fascinating virus-host interplay.
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Affiliation(s)
- Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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16
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Oh H, Jung Y, Moon S, Hwang J, Ban C, Chung J, Chung WJ, Kweon DH. Development of End-Spliced Dimeric Nanodiscs for the Improved Virucidal Activity of a Nanoperforator. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36757-36768. [PMID: 34319090 DOI: 10.1021/acsami.1c06364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lipid-bilayer nanodiscs (NDs) wrapped in membrane scaffold proteins (MSPs) have primarily been used to study membrane proteins of interest in a physiological environment. Recently, NDs have been employed in broader applications including drug delivery, cancer immunotherapy, bio-imaging, and therapeutic virucides. Here, we developed a method to synthesize a dimeric nanodisc, whose MSPs are circularly end-spliced, with long-term thermal stability and resistance to aggregation. The end-spliced nanodiscs (esNDs) were assembled using MSPs that were self-circularized inside the cytoplasm ofEscherichia colivia highly efficient protein trans-splicing. The esNDs demonstrated a consistent size and 4-5-fold higher stability against heat and aggregation than conventional NDs. Moreover, cysteine residues on trans-spliced circularized MSPs allowed us to modulate the formation of either monomeric nanodiscs (essNDs) or dimeric nanodiscs (esdNDs) by controlling the oxidation/reduction conditions and lipid-to-protein ratios. When the esdNDs were used to prepare an antiviral nanoperforator that induced the disruption of the viral membrane upon contact, antiviral activity was dramatically increased, suggesting that the dimerization of nanodiscs led to cooperativity between linked nanodiscs. We expect that controllable structures, long-term stability, and aggregation resistance of esNDs will aid the development of novel versatile membrane-mimetic nanomaterials with flexible designs and improved therapeutic efficacy.
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Affiliation(s)
- Hyunseok Oh
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Younghun Jung
- Institute of Biomolecular Control, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seokoh Moon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaehyeon Hwang
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Choongjin Ban
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Jinhyo Chung
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Woo-Jae Chung
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
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17
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Dixit U, Bhutoria S, Wu X, Qiu L, Spira M, Mathew S, Harris R, Adams LJ, Cahill S, Pathak R, Rajesh Kumar P, Nguyen M, Acharya SA, Brenowitz M, Almo SC, Zou X, Steven AC, Cowburn D, Girvin M, Kalpana GV. INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication. Nat Commun 2021; 12:2743. [PMID: 33980829 PMCID: PMC8115288 DOI: 10.1038/s41467-021-22733-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/24/2021] [Indexed: 11/09/2022] Open
Abstract
INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC50 values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.
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Affiliation(s)
- Updesh Dixit
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Savita Bhutoria
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Xuhong Wu
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Menachem Spira
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Sheeba Mathew
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Richard Harris
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Lucas J Adams
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - P Rajesh Kumar
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Minh Nguyen
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Seetharama A Acharya
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Mark Girvin
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Ganjam V Kalpana
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA.
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18
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Serrão VHB, Cook JD, Lee JE. Snapshot of an influenza virus glycoprotein fusion intermediate. Cell Rep 2021; 35:109152. [PMID: 34010634 DOI: 10.1016/j.celrep.2021.109152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Enveloped virus entry requires the fusion of cellular and viral membranes, a process directed by their viral fusion glycoproteins. Our current knowledge of this process has been shaped by structural studies of the pre- and post-fusion conformations of these viral fusogens. These structural snapshots have revealed the start and end states necessary for fusion, but the dynamics of the intermediate conformations have remained unclear. Using the influenza C virus hemagglutinin-esterase-fusion glycoprotein as a model, we report the structural and biophysical characterization of a trapped intermediate. Crystallographic studies revealed a structural reorganization of the C terminus to create a second chain reversal region, resulting in the N and C termini being positioned in opposing directions. Intrinsic tryptophan fluorescence and bimane-induced quenching measurements suggest intermediate formation is mediated by conserved hydrophobic residues. Our study reveals a late-stage extended intermediate structural event. This work adds to our understanding of virus cell fusion.
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Affiliation(s)
- Vitor Hugo B Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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19
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Kuchenbrod MT, Schubert US, Heintzmann R, Hoeppener S. Revisiting staining of biological samples for electron microscopy: perspectives for recent research. MATERIALS HORIZONS 2021; 8:685-699. [PMID: 34821312 DOI: 10.1039/d0mh01579b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This review revisits essential staining protocols for electron microscopy focussing on the visualization of active sites, i.e. enzymes, metabolites or proteins, in cells and tissues, which have been developed 50 to 60 years ago, however, never were established as standard protocols being used in electron microscopy in a routine fashion. These approaches offer numerous possibilities to expand the knowledge of cellular function and specifically address the localization of active compounds of these systems. It is our conviction, that many of these techniques are still useful, in particular when applied in conjunction with correlative light and electron microscopy. Revisiting specialized classical electron microscopy staining protocols for use in correlative microscopy is particularly promising, as some of these protocols were originally developed as staining methods for light microscopy. To account for this history, rather than summarizing the most recent achievements in literature, we instead first provide an overview of techniques that have been used in the past. While some of these techniques have been successfully implemented into modern microscopy techniques during recent years already, more possibilities are yet to be re-discovered and provide exciting new perspectives for their future use.
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Affiliation(s)
- Maren T Kuchenbrod
- Laboratory of Organic and Macromolecular Chemistry (IOMC) Friedrich Schiller University Jena, Humboldstr. 10, 07743, Germany.
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20
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Lu M. Single-Molecule FRET Imaging of Virus Spike-Host Interactions. Viruses 2021; 13:v13020332. [PMID: 33669922 PMCID: PMC7924862 DOI: 10.3390/v13020332] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
As a major surface glycoprotein of enveloped viruses, the virus spike protein is a primary target for vaccines and anti-viral treatments. Current vaccines aiming at controlling the COVID-19 pandemic are mostly directed against the SARS-CoV-2 spike protein. To promote virus entry and facilitate immune evasion, spikes must be dynamic. Interactions with host receptors and coreceptors trigger a cascade of conformational changes/structural rearrangements in spikes, which bring virus and host membranes in proximity for membrane fusion required for virus entry. Spike-mediated viral membrane fusion is a dynamic, multi-step process, and understanding the structure–function-dynamics paradigm of virus spikes is essential to elucidate viral membrane fusion, with the ultimate goal of interventions. However, our understanding of this process primarily relies on individual structural snapshots of endpoints. How these endpoints are connected in a time-resolved manner, and the order and frequency of conformational events underlying virus entry, remain largely elusive. Single-molecule Förster resonance energy transfer (smFRET) has provided a powerful platform to connect structure–function in motion, revealing dynamic aspects of spikes for several viruses: SARS-CoV-2, HIV-1, influenza, and Ebola. This review focuses on how smFRET imaging has advanced our understanding of virus spikes’ dynamic nature, receptor-binding events, and mechanism of antibody neutralization, thereby informing therapeutic interventions.
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Affiliation(s)
- Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
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21
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Heymann JB. High resolution electron tomography and segmentation-by-modeling interpretation in Bsoft. Protein Sci 2021; 30:44-59. [PMID: 32852078 PMCID: PMC7737767 DOI: 10.1002/pro.3938] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 11/11/2022]
Abstract
Bsoft offers many tools for the processing of tomographic tilt series and the interpretation of tomograms. Since I introduced tomography into Bsoft almost two decades ago, the field has advanced significantly, requiring refinement of old algorithms and development of new ones. The current direct detectors allow us to collect data more efficiently and with better quality, progressing towards automation. The goal is then to also automate alignment of tilt series and reconstruction. I added an estimation of the specimen thickness as well as fiducialless alignment, to augment the existing fiducial-based alignment. High-resolution work requires correction for the contrast transfer function, in tomography complicated by the tilted specimen. For this, I developed a method to generate a power spectrum using the whole micrograph, compensating for tilting. This is followed by routine determination of the contrast transfer function, and correction for it during reconstruction. The next steps involve interpretation of the tomogram, either by subtomogram averaging where possible, or by segmentation and modeling otherwise. Such interpretation actually constitutes the main time-consuming part of tomography and is less amenable to automation compared to the initial reconstruction.
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Affiliation(s)
- J. Bernard Heymann
- Laboratory for Structural Biology ResearchNational Institute of Arthritis, Musculoskeletal and Skin Diseases, NIHBethesdaMarylandUSA
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22
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Lim K, Kodera N, Wang H, Mohamed MS, Hazawa M, Kobayashi A, Yoshida T, Hanayama R, Yano S, Ando T, Wong RW. High-Speed AFM Reveals Molecular Dynamics of Human Influenza A Hemagglutinin and Its Interaction with Exosomes. NANO LETTERS 2020; 20:6320-6328. [PMID: 32787163 DOI: 10.1021/acs.nanolett.0c01755] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Influenza A hemagglutinin (HA) is one of the crucial virulence factors that mediate host tropism and viral infectivity. Presently, the mechanism of the fusogenic transition of HA remains elusive. Here, we used high-speed atomic force microscopy (HS-AFM) to decipher the molecular dynamics of HA and its interaction with exosomes. Our data reveal that the native conformation of HA in the neutral buffer is ellipsoidal, and HA undergoes a conformational change in an acidic buffer. Real-time visualization of the fusogenic transition by HS-AFM suggests that the mechanism is possibly fit to the "uncaging" model, and HA intermediate appears as Y-shaped. A firm interaction between the HA and exosome in an acidic buffer indicates the insertion of a fusion peptide into the exosomal layer and subsequently destabilizes the layer, resulting in the deformation or rupture of exosomes, releasing exosomal contents. In contrast, the HA-exosome interaction is weak in a neutral buffer because the interaction is mediated by weak bonds between the HA receptor-binding site and receptors on the exosome.
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Affiliation(s)
- Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hanbo Wang
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Mahmoud Shaaban Mohamed
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Yoshida
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Immunology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara, Kanazawa, Ishikawa 920-8640, Japan
| | - Rikinari Hanayama
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Immunology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara, Kanazawa, Ishikawa 920-8640, Japan
| | - Seiji Yano
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Richard W Wong
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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23
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Biswas M, Yamazaki T, Chiba J, Akashi-Takamura S. Broadly Neutralizing Antibodies for Influenza: Passive Immunotherapy and Intranasal Vaccination. Vaccines (Basel) 2020; 8:vaccines8030424. [PMID: 32751206 PMCID: PMC7565570 DOI: 10.3390/vaccines8030424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Influenza viruses cause annual epidemics and occasional pandemics. The high diversity of viral envelope proteins permits viruses to escape host immunity. Therefore, the development of a universal vaccine and broadly neutralizing antibodies (bnAbs) is essential for controlling various mutant viruses. Here, we review some potentially valuable bnAbs for influenza; one is a novel passive immunotherapy using a variable domain of heavy chain-only antibody (VHH), and the other is polymeric immunoglobulin A (pIgA) induced by intranasal vaccination. Recently, it was reported that a tetravalent multidomain antibody (MDAb) was developed by genetic fusion of four VHHs, which are bnAbs against the influenza A or B viruses. The transfer of a gene encoding the MDAb–Fc fusion protein provided cross-protection against both influenza A and B viruses in vivo. An intranasal universal influenza vaccine, which can induce neutralizing pIgAs in the upper respiratory tract, is currently undergoing clinical studies. A recent study has revealed that tetrameric IgAs formed in nasal mucosa are more broadly protective against influenza than the monomeric and dimeric forms. These broadly neutralizing antibodies have high potential to control the currently circulating influenza virus.
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Affiliation(s)
- Mrityunjoy Biswas
- Department of Microbiology and Immunology, School of Medicine, Aichi Medical University, Aichi 480-1195, Japan; (M.B.); (S.A.-T.)
| | - Tatsuya Yamazaki
- Department of Microbiology and Immunology, School of Medicine, Aichi Medical University, Aichi 480-1195, Japan; (M.B.); (S.A.-T.)
- Correspondence: ; Tel.: +81-56-162-3311
| | - Joe Chiba
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan;
| | - Sachiko Akashi-Takamura
- Department of Microbiology and Immunology, School of Medicine, Aichi Medical University, Aichi 480-1195, Japan; (M.B.); (S.A.-T.)
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24
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Benhaim MA, Mangala Prasad V, Garcia NK, Guttman M, Lee KK. Structural monitoring of a transient intermediate in the hemagglutinin fusion machinery on influenza virions. SCIENCE ADVANCES 2020; 6:eaaz8822. [PMID: 32494683 PMCID: PMC7190341 DOI: 10.1126/sciadv.aaz8822] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/05/2020] [Indexed: 05/16/2023]
Abstract
The influenza virus hemagglutinin (HA) fusion protein has long been viewed as a "spring-loaded" fusion machine whereby activation at low pH initiates a rapid and irreversible cascade of conformational changes that drives the membrane fusion reaction. This mechanism has shaped our understanding of how type 1 viral fusion proteins function as a whole. Experimental limitations have hindered efforts to expand our mechanistic and structural understanding of viral membrane fusion. Here, we used pulse-labeling hydrogen/deuterium exchange mass spectrometry and cryo-electron tomography to monitor and characterize the structural dynamics of HA during fusion activation on intact virions. Our data reveal how concurrent reorganizations at the HA1 receptor binding domain interface and HA2 fusion subunit produce a dynamic fusion intermediate ensemble in full-length HA. The soluble HA ectodomain transitions directly to the postfusion state with no observable intermediate.
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Affiliation(s)
- M. A. Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - V. Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - N. K. Garcia
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - M. Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - K. K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Corresponding author.
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25
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Jakubcová L, Vozárová M, Hollý J, Tomčíková K, Fogelová M, Polčicová K, Kostolanský F, Fodor E, Varečková E. Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. J Gen Virol 2020; 100:1282-1292. [PMID: 31329089 PMCID: PMC7414431 DOI: 10.1099/jgv.0.001305] [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] [Indexed: 01/13/2023] Open
Abstract
Influenza A viruses (IAVs) enter into cells by receptor-dependent endocytosis. Subsequently, conformational changes of haemagglutinin are triggered by low environmental pH and the N terminus of HA2 glycoprotein (gp) is inserted into the endosomal membrane, resulting in fusion pore formation and genomic vRNA release into the cytoplasm. However, the pH optimum of membrane fusion is host- and virus-specific and can have an impact on virus pathogenicity. We prepared mutants of neurotropic IAV A/WSN/33 (H1N1) with aa substitutions in HA2 gp at the site of HA1/HA2 interaction, namely T642H (HA2 numbering position 64, H1 numbering position HA407; referred to as mutant '64'), V662H ('66') (HA409); and a double mutant ('D') with two aa substitutions (T642H, V662H). These substitutions were hypothesized to influence the pH optimum of fusion. The pH optimum of fusion activity was measured by a luciferase assay and biological properties of viruses were monitored. The in vitro and in vivo replication ability and pathogenicity of mutants were comparable (64) or lower (66, D) than those of the wild-type virus. However, the HA2 mutation V662H and double mutation T642H, V662H shifted the fusion pH maximum to lower values (ranging from 5.1 to 5.3) compared to pH from 5.4 to 5.6 for the wild-type and 64 mutant. The decreased replication ability and pathogenicity of 66 and D mutants was accompanied by higher titres in late intervals post-infection in lungs, and viral RNA in brains compared to wild-type virus-infected mice. These results have implications for understanding the pathogenicity of influenza viruses.
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Affiliation(s)
- L Jakubcová
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - M Vozárová
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - J Hollý
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - K Tomčíková
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - M Fogelová
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - K Polčicová
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - F Kostolanský
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - E Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - E Varečková
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
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26
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Benhaim MA, Lee KK. New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes. Viruses 2020; 12:E413. [PMID: 32276357 PMCID: PMC7232462 DOI: 10.3390/v12040413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 12/27/2022] Open
Abstract
Protein-mediated membrane fusion is a highly regulated biological process essential for cellular and organismal functions and infection by enveloped viruses. During viral entry the membrane fusion reaction is catalyzed by specialized protein machinery on the viral surface. These viral fusion proteins undergo a series of dramatic structural changes during membrane fusion where they engage, remodel, and ultimately fuse with the host membrane. The structural and dynamic nature of these conformational changes and their impact on the membranes have long-eluded characterization. Recent advances in structural and biophysical methodologies have enabled researchers to directly observe viral fusion proteins as they carry out their functions during membrane fusion. Here we review the structure and function of type I viral fusion proteins and mechanisms of protein-mediated membrane fusion. We highlight how recent technological advances and new biophysical approaches are providing unprecedented new insight into the membrane fusion reaction.
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Affiliation(s)
- Mark A. Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA;
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA;
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA 98195-7610, USA
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27
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Asor R, Khaykelson D, Ben-Nun-Shaul O, Levi-Kalisman Y, Oppenheim A, Raviv U. pH stability and disassembly mechanism of wild-type simian virus 40. SOFT MATTER 2020; 16:2803-2814. [PMID: 32104873 PMCID: PMC7189960 DOI: 10.1039/c9sm02436k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Viruses are remarkable self-assembled nanobiomaterial-based machines, exposed to a wide range of pH values. Extreme pH values can induce dramatic structural changes, critical for the function of the virus nanoparticles, including assembly and genome uncoating. Tuning cargo-capsid interactions is essential for designing virus-based delivery systems. Here we show how pH controls the structure and activity of wild-type simian virus 40 (wtSV40) and the interplay between its cargo and capsid. Using cryo-TEM and solution X-ray scattering, we found that wtSV40 was stable between pH 5.5 and 9, and only slightly swelled with increasing pH. At pH 3, the particles aggregated, while capsid protein pentamers continued to coat the virus cargo but lost their positional correlations. Infectivity was only partly lost after the particles were returned to pH 7. At pH 10 or higher, the particles were unstable, lost their infectivity, and disassembled. Using time-resolved experiments we discovered that disassembly began by swelling of the particles, poking a hole in the capsid through which the genetic cargo escaped, followed by a slight shrinking of the capsids and complete disassembly. These findings provide insight into the fundamental intermolecular forces, essential for SV40 function, and for designing virus-based nanobiomaterials, including delivery systems and antiviral drugs.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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28
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Takeda Y, Okuyama Y, Nakano H, Yaoita Y, Machida K, Ogawa H, Imai K. Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:9-19. [PMID: 31620998 PMCID: PMC7223586 DOI: 10.1007/s12560-019-09408-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/01/2019] [Indexed: 05/28/2023]
Abstract
Influenza A virus (IAV) infection is perennially one of the leading causes of death worldwide. Effective therapy and vaccination are needed to control viral expansion. However, current anti-IAV drugs risk inducing drug-resistant virus emergence. Although intranasal administration of whole inactivated virus vaccine can induce efficient protective immunity, formalin and β-propiolactone are the currently used and harmful inactivating agents. Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. The in vitro study revealed that the pH of hibiscus tea extract is acidic, and its rapid and potent antiviral activity relied largely on the acidic pH. Furthermore, the mouse study showed that the acidic extract was not effective for either therapeutic or vaccination purposes. However, hibiscus tea extract and protocatechuic acid, one of the major components of the extract, showed not only potent acid-dependent antiviral activity but also weak low-pH-independent activity. The low-pH-independent activity did not affect the conformation of immunodominant hemagglutinin protein. Although this low-pH-independent activity is very limited, it may be suitable for the application to medication and vaccination because this activity is not affected by the neutral blood environment and does not lose antigenicity of hemagglutinin. Further study of the low-pH-independent antiviral mechanism and attempts to enhance the antiviral activity may establish a novel anti-IAV therapy and vaccination strategy.
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Affiliation(s)
- Yohei Takeda
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan
| | - Yuko Okuyama
- Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, 981-8558, Japan
| | - Hiroto Nakano
- Division of Sustainable and Environmental Engineering, Graduate School of Engineering, Muroran Institute of Technology, 27-1 Mizumoto, Muroran, 050-8585, Japan
| | - Yasunori Yaoita
- Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, 981-8558, Japan
| | - Koich Machida
- Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, 981-8558, Japan
| | - Haruko Ogawa
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan.
| | - Kunitoshi Imai
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan
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29
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Matsubara T, Ujie M, Yamamoto T, Einaga Y, Daidoji T, Nakaya T, Sato T. Avian Influenza Virus Detection by Optimized Peptide Termination on a Boron-Doped Diamond Electrode. ACS Sens 2020; 5:431-439. [PMID: 32077684 DOI: 10.1021/acssensors.9b02126] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development of a simple detection method with high sensitivity is essential for the diagnosis and surveillance of infectious diseases. Previously, we constructed a sensitive biosensor for the detection of pathological human influenza viruses using a boron-doped diamond electrode terminated with a sialyloligosaccharide receptor-mimic peptide that could bind to hemagglutinins involved in viral infection. Circulation of influenza induced by the avian virus in humans has become a major public health concern, and methods for the detection of avian viruses are urgently needed. Here, peptide density and dendrimer generation terminated on the electrode altered the efficiency of viral binding to the electrode surface, thus significantly enhancing charge-transfer resistance measured by electrochemical impedance spectroscopy. The peptide-terminated electrodes exhibited an excellent detection limit of less than one plaque-forming unit of seasonal H1N1 and H3N2 viruses. Furthermore, the improved electrode was detectable for avian viruses isolated from H5N3, H7N1, and H9N2, showing the potential for the detection of all subtypes of influenza A virus, including new subtypes. The peptide-based electrochemical architecture provided a promising approach to biosensors for ultrasensitive detection of pathogenic microorganisms.
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Affiliation(s)
- Teruhiko Matsubara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Michiko Ujie
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Takashi Yamamoto
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yasuaki Einaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- JST-ACCEL, 5, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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30
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Li B, Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, Smith N, Regan T, Farr D, Gutmann MU, Bukhari SI, Law A, Sangesland M, Gat-Viks I, Digard P, Vasudevan S, Lingwood D, Dockrell DH, Doench JG, Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nat Commun 2020; 11:164. [PMID: 31919360 PMCID: PMC6952391 DOI: 10.1038/s41467-019-13965-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Host dependency factors that are required for influenza A virus infection may serve as therapeutic targets as the virus is less likely to bypass them under drug-mediated selection pressure. Previous attempts to identify host factors have produced largely divergent results, with few overlapping hits across different studies. Here, we perform a genome-wide CRISPR/Cas9 screen and devise a new approach, meta-analysis by information content (MAIC) to systematically combine our results with prior evidence for influenza host factors. MAIC out-performs other meta-analysis methods when using our CRISPR screen as validation data. We validate the host factors, WDR7, CCDC115 and TMEM199, demonstrating that these genes are essential for viral entry and regulation of V-type ATPase assembly. We also find that CMTR1, a human mRNA cap methyltransferase, is required for efficient viral cap snatching and regulation of a cell autonomous immune response, and provides synergistic protection with the influenza endonuclease inhibitor Xofluza. Here, Li et al. perform a genome-wide CRISPR screen to identify host dependency factors for influenza A virus infection and show that the host mRNA cap methyltransferase CMTR1 is important for viral cap snatching and that it affects expression of antiviral genes.
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Affiliation(s)
- Bo Li
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sara M Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Bing Shao Chia
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Ang Cui
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas Eisenhaure
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Paul Hoover
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nikki Smith
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tim Regan
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - David Farr
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Michael U Gutmann
- School of informatics, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Syed Irfan Bukhari
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Irit Gat-Viks
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Paul Digard
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Shobha Vasudevan
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - David H Dockrell
- MRC Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - John G Doench
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, EH16 5SA, UK.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. .,Massachusetts General Hospital Cancer Center, Boston, MA, 02129, USA.
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31
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Antanasijevic A, Durst MA, Lavie A, Caffrey M. Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography. J Struct Biol 2019; 209:107412. [PMID: 31689502 PMCID: PMC7111647 DOI: 10.1016/j.jsb.2019.107412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/15/2022]
Abstract
X-ray crystallography identifies a conserved histidine, HA1-H38, that changes side chain conformation at low pH. We attribute the observed conformational change to cation-cation repulsion between protonated HA1-H18 and HA1-H38. We suggest that the HA1-H18 and HA1-H38 pair plays a role in the pathway toward the postfusion conformation of HA.
Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in Group 1 HA, undergoes a striking change in side chain conformation, which we attribute to its protonation and cation-cation repulsion with conserved HA1-H18. This work suggests that x-ray crystallography can be applied for studying small-scale pH-induced conformational changes providing valuable information on the location of pH sensors in HA. Importantly, the observed change in HA1-H38 conformation is further evidence that the pH-induced conformational changes of HA are the result of a series of protonation events to conserved and non-conserved pH sensors.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA
| | - Matthew A Durst
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA.
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA.
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32
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The application of atomic force microscopy for viruses and protein shells: Imaging and spectroscopy. Adv Virus Res 2019; 105:161-187. [PMID: 31522704 DOI: 10.1016/bs.aivir.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic force microscopy (AFM) probes surface-adsorbed samples at the nanoscale by using a sharp stylus of nanometric size located at the end of a micro-cantilever. This technique can also work in a liquid environment and offers unique possibilities to study individual protein assemblies, such as viruses, under conditions that resemble their natural liquid milieu. Here, I show how AFM can be used to explore the topography of viruses and protein cages, including that of structures lacking a well-defined symmetry. AFM is not limited for imaging and allows the manipulation of individual viruses with force spectroscopy approaches, such as single indentation and mechanical fatigue assays. These pushing experiments deform the protein cages to obtain their mechanical information and can be used to monitor the structural changes induced by maturation or the exposure to different biochemical environments, such as pH variation. We discuss how studying capsid rupture and self-healing events offers insight into virus uncoating pathways. On the other hand, pulling tests can provide information about the virus-host interaction established between the viral fibers and the cell membrane.
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33
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Kosik I, Yewdell JW. Influenza Hemagglutinin and Neuraminidase: Yin⁻Yang Proteins Coevolving to Thwart Immunity. Viruses 2019; 11:E346. [PMID: 31014029 PMCID: PMC6520700 DOI: 10.3390/v11040346] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 01/04/2023] Open
Abstract
Influenza A virions possess two surface glycoproteins-the hemagglutinin (HA) and neuraminidase (NA)-which exert opposite functions. HA attaches virions to cells by binding to terminal sialic acid residues on glycoproteins/glycolipids to initiate the infectious cycle, while NA cleaves terminal sialic acids, releasing virions to complete the infectious cycle. Antibodies specific for HA or NA can protect experimental animals from IAV pathogenesis and drive antigenic variation in their target epitopes that impairs vaccine effectiveness in humans. Here, we review progress in understanding HA/NA co-evolution as each acquires epistatic mutations to restore viral fitness to mutants selected in the other protein by host innate or adaptive immune pressure. We also discuss recent exciting findings that antibodies to HA can function in vivo by blocking NA enzyme activity to prevent nascent virion release and enhance Fc receptor-based activation of innate immune cells.
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Affiliation(s)
- Ivan Kosik
- Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD 20892, USA.
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34
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Benhaim M, Lee KK. Single-Molecule Analysis of a Viral Fusion Protein Illuminates a Fusion-Active Intermediate State. Cell 2019; 174:775-777. [PMID: 30096307 DOI: 10.1016/j.cell.2018.07.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The influenza virus hemagglutinin (HA) fusion glycoprotein mediates viral entry into host cells through its receptor binding and membrane fusion activities. In this issue of Cell, Das et al. use single-molecule Förster resonance energy transfer (smFRET) to monitor HA conformational dynamics. Their study reveals this prototypical class I fusion protein to be a highly dynamic molecule capable of reversibly sampling multiple states, including on-pathway fusion intermediates between pre-fusion and post-fusion endpoints. These findings challenge long-held ideas for how HA functions and move the field closer to obtaining a mechanistic understanding of how class I fusion proteins mediate membrane fusion.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Biological Physics Structure and Design Program, University of Washington, Seattle, WA 98195, USA.
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35
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de Pablo PJ, Schaap IAT. Atomic Force Microscopy of Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:159-179. [PMID: 31317500 DOI: 10.1007/978-3-030-14741-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Atomic force microscopy employs a nanometric tip located at the end of a micro-cantilever to probe surface-mounted samples at nanometer resolution. Because the technique can also work in a liquid environment it offers unique possibilities to study individual viruses under conditions that mimic their natural milieu. Here, we review how AFM imaging can be used to study the surface structure of viruses including that of viruses lacking a well-defined symmetry. Beyond imaging, AFM enables the manipulation of single viruses by force spectroscopy experiments. Pulling experiments can provide information about the early events of virus-host interaction between the viral fibers and the cell membrane receptors. Pushing experiments measure the mechanical response of the viral capsid and its contents and can be used to show how virus maturation and exposure to different pH values change the mechanical response of the viruses and the interaction between the capsid and genome. Finally, we discuss how studying capsid rupture and self-healing events offers insight in virus uncoating pathways.
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Affiliation(s)
- P J de Pablo
- Department of Condensed Matter Physics and Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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36
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Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation. mBio 2018; 9:mBio.01567-18. [PMID: 30327442 PMCID: PMC6191540 DOI: 10.1128/mbio.01567-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Late in the HIV-1 replication cycle, the viral structural protein Gag is targeted to virus assembly sites at the plasma membrane of infected cells. The capsid (CA) domain of Gag plays a critical role in the formation of the hexameric Gag lattice in the immature virion, and, during particle release, CA is cleaved from the Gag precursor by the viral protease and forms the conical core of the mature virion. A highly conserved Pro-Pro-Ile-Pro (PPIP) motif (CA residues 122 to 125) [PPIP(122-125)] in a loop connecting CA helices 6 and 7 resides at a 3-fold axis formed by neighboring hexamers in the immature Gag lattice. In this study, we characterized the role of this PPIP(122-125) loop in HIV-1 assembly and maturation. While mutations P123A and P125A were relatively well tolerated, mutation of P122 and I124 significantly impaired virus release, caused Gag processing defects, and abolished infectivity. X-ray crystallography indicated that the P122A and I124A mutations induce subtle changes in the structure of the mature CA lattice which were permissive for in vitro assembly of CA tubes. Transmission electron microscopy and cryo-electron tomography demonstrated that the P122A and I124A mutations induce severe structural defects in the immature Gag lattice and abrogate conical core formation. Propagation of the P122A and I124A mutants in T-cell lines led to the selection of compensatory mutations within CA. Our findings demonstrate that the CA PPIP(122-125) loop comprises a structural element critical for the formation of the immature Gag lattice.IMPORTANCE Capsid (CA) plays multiple roles in the HIV-1 replication cycle. CA-CA domain interactions are responsible for multimerization of the Gag polyprotein at virus assembly sites, and in the mature virion, CA monomers assemble into a conical core that encapsidates the viral RNA genome. Multiple CA regions that contribute to the assembly and release of HIV-1 particles have been mapped and investigated. Here, we identified and characterized a Pro-rich loop in CA that is important for the formation of the immature Gag lattice. Changes in this region disrupt viral production and abrogate the formation of infectious, mature virions. Propagation of the mutants in culture led to the selection of second-site compensatory mutations within CA. These results expand our knowledge of the assembly and maturation steps in the viral replication cycle and may be relevant for development of antiviral drugs targeting CA.
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Das DK, Govindan R, Nikić-Spiegel I, Krammer F, Lemke EA, Munro JB. Direct Visualization of the Conformational Dynamics of Single Influenza Hemagglutinin Trimers. Cell 2018; 174:926-937.e12. [PMID: 29961575 PMCID: PMC6086748 DOI: 10.1016/j.cell.2018.05.050] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/02/2023]
Abstract
Influenza hemagglutinin (HA) is the canonical type I viral envelope glycoprotein and provides a template for the membrane-fusion mechanisms of numerous viruses. The current model of HA-mediated membrane fusion describes a static "spring-loaded" fusion domain (HA2) at neutral pH. Acidic pH triggers a singular irreversible conformational rearrangement in HA2 that fuses viral and cellular membranes. Here, using single-molecule Förster resonance energy transfer (smFRET)-imaging, we directly visualized pH-triggered conformational changes of HA trimers on the viral surface. Our analyses reveal reversible exchange between the pre-fusion and two intermediate conformations of HA2. Acidification of pH and receptor binding shifts the dynamic equilibrium of HA2 in favor of forward progression along the membrane-fusion reaction coordinate. Interaction with the target membrane promotes irreversible transition of HA2 to the post-fusion state. The reversibility of HA2 conformation may protect against transition to the post-fusion state prior to arrival at the target membrane.
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Affiliation(s)
- Dibyendu Kumar Das
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA.
| | - Ramesh Govindan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tuebingen, 72076 Tuebingen, Germany
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy, and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA.
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B Carvalho S, Fortuna AR, Wolff MW, Peixoto C, M Alves P, Reichl U, JT Carrondo M. Purification of influenza virus-like particles using sulfated cellulose membrane adsorbers. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2018; 93:1988-1996. [PMID: 30008506 PMCID: PMC6033026 DOI: 10.1002/jctb.5474] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/30/2017] [Accepted: 10/01/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND Vaccines based on virus-like particles (VLPs) are an alternative to inactivated viral vaccines that combine good safety profiles with strong immunogenicity. In order to be economically competitive, efficient manufacturing is required, in particular downstream processing, which often accounts for major production costs. This study describes the optimization and establishment of a chromatography capturing technique using sulfated cellulose membrane adsorbers (SCMA) for purification of influenza VLPs. RESULTS Using a design of experiments approach, the critical factors for SCMA performance were described and optimized. For optimal conditions (membrane ligand density: 15.4 µmol cm-2, salt concentration of the loading buffer: 24 mmol L-1 NaCl, and elution buffer: 920 mmol L-1 NaCl, as well as the corresponding flow rates: 0.24 and 1.4 mL min-1), a yield of 80% in the product fraction was obtained. No loss of VLPs was detected in the flowthrough fraction. Removal of total protein and DNA impurities were higher than 89% and 80%, respectively. CONCLUSION Use of SCMA represents a significant improvement compared with conventional ion exchanger membrane adsorbers. As the method proposed is easily scalable and reduces the number of steps required compared with conventional purification methods, SCMA could qualify as a generic platform for purification of VLP-based influenza vaccines. © 2017 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Sofia B Carvalho
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - A Raquel Fortuna
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Michael W Wolff
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
- Institute of Bioprocess Engineering and Pharmaceutical TechnologyUniversity of Applied Sciences MittelhessenGießenGermany
| | - Cristina Peixoto
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaOeirasPortugal
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
- Otto von Guericke University MagdeburgMagdeburgGermany
| | - Manuel JT Carrondo
- iBET, Instituto de Biologia Experimental e TecnológicaOeirasPortugal
- Departamento de Química, Faculdade de Ciências e TecnologiaUniversidade Nova de LisboaCaparicaPortugal
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Gamage S, Howard M, Makita H, Cross B, Hastings G, Luo M, Abate Y. Probing structural changes in single enveloped virus particles using nano-infrared spectroscopic imaging. PLoS One 2018; 13:e0199112. [PMID: 29894493 PMCID: PMC5997350 DOI: 10.1371/journal.pone.0199112] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 01/26/2023] Open
Abstract
Enveloped viruses, such as HIV, Ebola and Influenza, are among the most deadly known viruses. Cellular membrane penetration of enveloped viruses is a critical step in the cascade of events that lead to entry into the host cell. Conventional ensemble fusion assays rely on collective responses to membrane fusion events, and do not allow direct and quantitative studies of the subtle and intricate fusion details. Such details are accessible via single particle investigation techniques, however. Here, we implement nano-infrared spectroscopic imaging to investigate the chemical and structural modifications that occur prior to membrane fusion in the single archetypal enveloped virus, influenza X31. We traced in real-space structural and spectroscopic alterations that occur during environmental pH variations in single virus particles. In addition, using nanospectroscopic imaging we quantified the effectiveness of an antiviral compound in stopping viral membrane disruption (a novel mechanism for inhibiting viral entry into cells) during environmental pH variations.
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Affiliation(s)
- Sampath Gamage
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia, United States of America
| | - Marquez Howard
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia, United States of America
| | - Hiroki Makita
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia, United States of America
| | - Brendan Cross
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia, United States of America
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia, United States of America
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
| | - Yohannes Abate
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Gallagher JR, McCraw DM, Torian U, Gulati NM, Myers ML, Conlon MT, Harris AK. Characterization of Hemagglutinin Antigens on Influenza Virus and within Vaccines Using Electron Microscopy. Vaccines (Basel) 2018; 6:E31. [PMID: 29799445 PMCID: PMC6027289 DOI: 10.3390/vaccines6020031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/08/2023] Open
Abstract
Influenza viruses affect millions of people worldwide on an annual basis. Although vaccines are available, influenza still causes significant human mortality and morbidity. Vaccines target the major influenza surface glycoprotein hemagglutinin (HA). However, circulating HA subtypes undergo continual variation in their dominant epitopes, requiring vaccines to be updated annually. A goal of next-generation influenza vaccine research is to produce broader protective immunity against the different types, subtypes, and strains of influenza viruses. One emerging strategy is to focus the immune response away from variable epitopes, and instead target the conserved stem region of HA. To increase the display and immunogenicity of the HA stem, nanoparticles are being developed to display epitopes in a controlled spatial arrangement to improve immunogenicity and elicit protective immune responses. Engineering of these nanoparticles requires structure-guided design to optimize the fidelity and valency of antigen presentation. Here, we review electron microscopy applied to study the 3D structures of influenza viruses and different vaccine antigens. Structure-guided information from electron microscopy should be integrated into pipelines for the development of both more efficacious seasonal and universal influenza vaccine antigens. The lessons learned from influenza vaccine electron microscopic research could aid in the development of novel vaccines for other pathogens.
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Affiliation(s)
- John R Gallagher
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Dustin M McCraw
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Udana Torian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Neetu M Gulati
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Mallory L Myers
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Michael T Conlon
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Audray K Harris
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
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Chen X, Liu S, Goraya MU, Maarouf M, Huang S, Chen JL. Host Immune Response to Influenza A Virus Infection. Front Immunol 2018; 9:320. [PMID: 29556226 PMCID: PMC5845129 DOI: 10.3389/fimmu.2018.00320] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/05/2018] [Indexed: 12/25/2022] Open
Abstract
Influenza A viruses (IAVs) are contagious pathogens responsible for severe respiratory infection in humans and animals worldwide. Upon detection of IAV infection, host immune system aims to defend against and clear the viral infection. Innate immune system is comprised of physical barriers (mucus and collectins), various phagocytic cells, group of cytokines, interferons (IFNs), and IFN-stimulated genes, which provide first line of defense against IAV infection. The adaptive immunity is mediated by B cells and T cells, characterized with antigen-specific memory cells, capturing and neutralizing the pathogen. The humoral immune response functions through hemagglutinin-specific circulating antibodies to neutralize IAV. In addition, antibodies can bind to the surface of infected cells and induce antibody-dependent cell-mediated cytotoxicity or complement activation. Although there are neutralizing antibodies against the virus, cellular immunity also plays a crucial role in the fight against IAVs. On the other hand, IAVs have developed multiple strategies to escape from host immune surveillance for successful replication. In this review, we discuss how immune system, especially innate immune system and critical molecules are involved in the antiviral defense against IAVs. In addition, we highlight how IAVs antagonize different immune responses to achieve a successful infection.
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Affiliation(s)
- Xiaoyong Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shasha Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mohsan Ullah Goraya
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
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Boonstra S, Blijleven JS, Roos WH, Onck PR, van der Giessen E, van Oijen AM. Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective. Annu Rev Biophys 2018; 47:153-173. [PMID: 29494252 DOI: 10.1146/annurev-biophys-070317-033018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.
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Affiliation(s)
- Sander Boonstra
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Jelle S Blijleven
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Antoine M van Oijen
- School of Chemistry; Faculty of Science, Medicine and Health; University of Wollongong, Wollongong, New South Wales 2522, Australia;
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Dissection of Epitope-Specific Mechanisms of Neutralization of Influenza Virus by Intact IgG and Fab Fragments. J Virol 2018; 92:JVI.02006-17. [PMID: 29263254 DOI: 10.1128/jvi.02006-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/08/2017] [Indexed: 11/20/2022] Open
Abstract
The neutralizing antibody (nAb) response against the influenza virus hemagglutinin (HA) fusion glycoprotein is important for preventing viral infection, but we lack a comprehensive understanding of the mechanisms by which these antibodies act. Here we investigated the effect of nAb binding and the role of IgG bivalency in the inhibition of HA function for nAbs targeting distinct HA epitopes. HC19 targets the receptor binding pocket at the distal end of HA, while FI6v3 binds primarily to the HA2 fusion subunit toward the base of the stalk. Surprisingly, HC19 inhibited the ability of HA to induce lipid mixing by preventing the structural rearrangement of HA under fusion-activating conditions. These results suggest that nAbs such as HC19 not only act by blocking receptor binding but also inhibit key late-stage HA conformational changes required for fusion. Intact HC19 IgG was also shown to cross-link separate virus particles, burying large proportions of HA within aggregates where they are blocked from interacting with target membranes; Fabs yielded no such aggregation and displayed weaker neutralization than IgG, emphasizing the impact of bivalency on the ability to neutralize virus. In contrast, the stem-targeting nAb FI6v3 did not aggregate particles. The Fab fragment was significantly less effective than IgG in preventing both membrane disruption and fusion. We infer that interspike cross-linking within a given particle by FI6v3 IgG may be critical to its potent neutralization, as no significant neutralization occurred with Fabs. These results demonstrate that IgG bivalency enhances HA inhibition through functionally important modes not evident in pared-down Fab-soluble HA structures.IMPORTANCE The influenza virus hemagglutinin (HA) fusion glycoprotein mediates entry into target cells and is the primary antigenic target of neutralizing antibodies (nAbs). Our current structural understanding of mechanisms of antibody (Ab)-mediated neutralization largely relies on the high-resolution characterization of antigen binding (Fab) fragments in complex with soluble, isolated antigen constructs by cryo-electron microscopy (EM) single-particle reconstruction or X-ray crystallography. Interactions between full-length IgG and whole virions have not been well characterized, and a gap remains in our understanding of how intact Abs neutralize virus and prevent infection. Using structural and biophysical approaches, we observed that Ab-mediated inhibition of HA function and neutralization of virus infectivity occur by multiple coexisting mechanisms, are largely dependent on the specific epitope that is targeted, and are highly dependent on the bivalent nature of IgG molecules.
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Kordyukova LV, Shtykova EV, Baratova LA, Svergun DI, Batishchev OV. Matrix proteins of enveloped viruses: a case study of Influenza A virus M1 protein. J Biomol Struct Dyn 2018; 37:671-690. [PMID: 29388479 DOI: 10.1080/07391102.2018.1436089] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Influenza A virus, a member of the Orthomyxoviridae family of enveloped viruses, is one of the human and animal top killers, and its structure and components are therefore extensively studied during the last decades. The most abundant component, M1 matrix protein, forms a matrix layer (scaffold) under the viral lipid envelope, and the functional roles as well as structural peculiarities of the M1 protein are still under heavy debate. Despite multiple attempts of crystallization, no high resolution structure is available for the full length M1 of Influenza A virus. The likely reason for the difficulties lies in the intrinsic disorder of the M1 C-terminal part preventing diffraction quality crystals to be grown. Alternative structural methods including synchrotron small-angle X-ray scattering (SAXS), atomic force microscopy, cryo-electron microscopy/tomography are therefore widely applied to understand the structure of M1, its self-association and interactions with the lipid membrane and the viral nucleocapsid. These methods reveal striking similarities in the behavior of M1 and matrix proteins of other enveloped RNA viruses, with the differences accompanied by the specific features of the viral lifecycles, thus suggesting common interaction principles and, possibly, common evolutional ancestors. The structural information on the Influenza A virus M1 protein obtained to the date strongly suggests that the intrinsic disorder in the C-terminal domain has important functional implications.
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Affiliation(s)
- Larisa V Kordyukova
- a Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Eleonora V Shtykova
- b Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences , Moscow , Russian Federation.,c Semenov Institute of Chemical Physics , Russian Academy of Sciences , Moscow , Russian Federation
| | - Lyudmila A Baratova
- a Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | | | - Oleg V Batishchev
- e Frumkin Institute of Physical Chemistry and Electrochemistry , Russian Academy of Sciences , Moscow , Russian Federation.,f Moscow Institute of Physics and Technology , Dolgoprudniy , Russian Federation
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Chiang MJ, Musayev FN, Kosikova M, Lin Z, Gao Y, Mosier PD, Althufairi B, Ye Z, Zhou Q, Desai UR, Xie H, Safo MK. Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Emerg Microbes Infect 2017; 6:e108. [PMID: 29209052 PMCID: PMC5750462 DOI: 10.1038/emi.2017.96] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/25/2017] [Accepted: 10/15/2017] [Indexed: 12/31/2022]
Abstract
The M gene segment of influenza A virus has been shown to be a contributing factor to the high growth phenotype. However, it remains largely unknown why matrix protein 1 (M1), the major structural protein encoded by M gene, exhibits pH-dependent conformational changes during virus replication. Understanding the mechanisms underlying efficient virus replication can help to develop strategies not only to combat influenza infections but also to improve vaccine supplies. M(NLS-88R) and M(NLS-88E) are two M1 mutants differing by only a single amino acid: G88R vs G88E. G88R but not G88E was the compensatory mutation naturally selected by the virus after its nuclear localization signal was disrupted. Our study shows that, compared with M(NLS-88E) M1, M(NLS-88R) M1 dissociated quickly from viral ribonucleoproteins (vRNPs) at higher pH and took less time to dissemble in vitro, despite forming thicker matrix layer and having stronger association with vRNP in assembled virions. Correspondingly, M(NLS-88R) replicated more efficiently and was genetically more stable than M(NLS-88E). Crystallographic analysis indicated that M(NLS-88R) M1, like wild-type M1, is able to switch from a face-to-back-oriented conformation to a face-to-face-oriented conformation when pH drops from neutral to acidic, whereas G88E mutation causes M(NLS-88E) M1 to be trapped in a face-to-face-arranged conformation regardless of environmental pH. Our results suggest that maintaining M1 pH-dependent conformational flexibility is critical for efficient virus replication, and position 88 is a key residue controlling M1 pH-dependent conformational changes. Our findings provide insights into developing M1-based antiviral agents.
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Affiliation(s)
- Meng-Jung Chiang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Faik N Musayev
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Martina Kosikova
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Zhengshi Lin
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yamei Gao
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Philip D Mosier
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bashayer Althufairi
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Zhiping Ye
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Qibing Zhou
- Department of Nanomedicine and Biopharmaceuticals, National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Hang Xie
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Martin K Safo
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
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Zhou JS, Chen AYS, Drucker M, Lopez NH, Carpenter A, Ng JCK. Whitefly feeding behavior and retention of a foregut-borne crinivirus exposed to artificial diets with different pH values. INSECT SCIENCE 2017; 24:1079-1092. [PMID: 28677320 DOI: 10.1111/1744-7917.12503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/08/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Transmission of plant viruses by phytophagous hemipteran insects encompasses complex interactions underlying a continuum of processes involved in virus acquisition, retention and inoculation combined with vector feeding behavior. Here, we investigated the effects of dietary pH on whitefly (Bemisia tabaci) feeding behavior and release of Lettuce infectious yellows virus (LIYV) virions retained in the vector's foregut. Electrical penetration graph analysis revealed that variables associated with whitefly probing and ingestion did not differ significantly in pH (4, 7.4, and 9) adjusted artificial diets. To investigate virus retention and release, whiteflies allowed to acquire LIYV virions in a pH 7.4 artificial diet were fed pH 4, 7.4, or 9 virion-free artificial (clearing) diets. Immunofluorescent localization analyses indicated that virions remained bound to the foreguts of approximately 20%-24% of vectors after they fed on each of the 3 pH-adjusted clearing diets. When RNA preparations from the clearing diets were analyzed by reverse transcription (RT) nested-PCR and, in some cases, real-time qPCR, successful amplification of LIYV-specific sequence was infrequent but consistently repeatable for the pH 7.4 diet but never observed for the pH 4 and 9 diets, suggesting a weak pH-dependent effect for virion release. Viruliferous vectors that fed on each of the 3 pH-adjusted clearing diets transmitted LIYV to virus-free plants. These results suggest that changes in pH values alone in artificial diet do not result in observable changes in whitefly feeding behaviors, an observation that marks a first in the feeding of artificial diet by whitefly vectors; and that there is a potential causal and contingent relationship between the pH in artificial diet and the release/inoculation of foregut bound virions.
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Affiliation(s)
- Jaclyn S Zhou
- Department of Plant Pathology and Microbiology, and Center for Disease Vector Research, University of California, Riverside, California, USA
| | - Angel Y S Chen
- Department of Plant Pathology and Microbiology, and Center for Disease Vector Research, University of California, Riverside, California, USA
| | - Martin Drucker
- INRA, UMR BGPI Plant Pathogen Interactions, Montpellier Cedex 5, France
| | | | | | - James C K Ng
- Department of Plant Pathology and Microbiology, and Center for Disease Vector Research, University of California, Riverside, California, USA
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Improvement of a rapid diagnostic application of monoclonal antibodies against avian influenza H7 subtype virus using Europium nanoparticles. Sci Rep 2017; 7:7933. [PMID: 28801679 PMCID: PMC5554140 DOI: 10.1038/s41598-017-08328-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/07/2017] [Indexed: 01/19/2023] Open
Abstract
The development of a sensitive and rapid diagnostic test is needed for early detection of avian influenza (AI) H7 subtype. In this study, novel monoclonal antibodies (mAbs) against influenza A H7N9 recombinant hemagglutinin (rHA)1 were developed and applied to a Europium nanoparticle–based rapid fluorescent immunochromatographic strip test (FICT) to improve the sensitivity of the rapid diagnostic system. Two antibodies (2F4 and 6D7) exhibited H7 subtype specificity in a dot-FICT assay by optimization of the conjugate and the pH of the lysis buffer. The subtype specificity was confirmed by an immunofluorescence assay and Western blot analysis. The limit of detection of the FICT employing novel mAbs 31 ng/mL for H7N9 rHA1 and 40 hemagglutination units/mL for H7 subtype virus. Sensitivity was improved 25-fold using Europium as confirmed by comparison of colloidal gold-based rapid diagnostic kit using the 2F4 and 6D7 mAbs.
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48
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Di Lella S, Herrmann A, Mair CM. Modulation of the pH Stability of Influenza Virus Hemagglutinin: A Host Cell Adaptation Strategy. Biophys J 2017; 110:2293-2301. [PMID: 27276248 DOI: 10.1016/j.bpj.2016.04.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/15/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Proteins undergo dynamic structural changes to function within the range of physical and chemical conditions of their microenvironments. Changes in these environments affect their activity unless the respective mutations preserve their proper function. Here, we examine the influenza A virus spike protein hemagglutinin (HA), which undergoes a dynamic conformational change that is essential to the viral life cycle and is dependent on endosomal pH. Since the cells of different potential hosts exhibit different levels of pH, the virus can only cross species barriers if HA undergoes mutations that still permit the structural change to occur. This key event occurs after influenza A enters the host cell via the endocytic route, during its intracellular transport inside endosomes. The acidic pH inside these vesicles triggers a major structural transition of HA that induces fusion of the viral envelope and the endosomal membrane, and permits the release of the viral genome. HA experiences specific mutations that alter its pH stability and allow the conformational changes required for fusion in different hosts, despite the differences in the degree of acidification of their endosomes. Experimental and theoretical studies over the past few years have provided detailed insights into the structural aspects of the mutational changes that alter its susceptibility to different pH thresholds. We will illustrate how such mutations modify the protein's structure and consequently its pH stability. These changes make HA an excellent model of the way subtle structural modifications affect a protein's stability and enable it to function in diverse environments.
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Affiliation(s)
- Santiago Di Lella
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany; Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Andreas Herrmann
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Caroline M Mair
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
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Lee J, Kim J, Son K, d'Alexandry d'Orengiani ALPH, Min JY. Acid phosphatase 2 (ACP2) is required for membrane fusion during influenza virus entry. Sci Rep 2017; 7:43893. [PMID: 28272419 PMCID: PMC5341025 DOI: 10.1038/srep43893] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023] Open
Abstract
Influenza viruses exploit host factors to successfully replicate in infected cells. Using small interfering RNA (siRNA) technology, we identified six human genes required for influenza A virus (IAV) replication. Here we focused on the role of acid phosphatase 2 (ACP2), as its knockdown showed the greatest inhibition of IAV replication. In IAV-infected cells, depletion of ACP2 resulted in a significant reduction in the expression of viral proteins and mRNA, and led to the attenuation of virus multi-cycle growth. ACP2 knockdown also decreased replication of seasonal influenza A and B viruses and avian IAVs of the H7 subtype. Interestingly, ACP2 depletion had no effect on the replication of Ebola or hepatitis C virus. Because ACP2 is known to be a lysosomal acid phosphatase, we assessed the role of ACP2 in influenza virus entry. While neither binding of the viral particle to the cell surface nor endosomal acidification was affected in ACP2-depleted cells, fusion of the endosomal and viral membranes was impaired. As a result, downstream steps in viral entry were blocked, including nucleocapsid uncoating and nuclear import of viral ribonucleoproteins. Our results established ACP2 as a necessary host factor for regulating the fusion step of influenza virus entry.
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Affiliation(s)
- Jihye Lee
- Respiratory Viruses Research Laboratory, Discovery Biology Department, Institut Pasteur Korea, Seongnam, Gyeonggi, Republic of Korea
| | - Jinhee Kim
- Respiratory Viruses Research Laboratory, Discovery Biology Department, Institut Pasteur Korea, Seongnam, Gyeonggi, Republic of Korea
| | - Kidong Son
- Respiratory Viruses Research Laboratory, Discovery Biology Department, Institut Pasteur Korea, Seongnam, Gyeonggi, Republic of Korea
| | | | - Ji-Young Min
- Respiratory Viruses Research Laboratory, Discovery Biology Department, Institut Pasteur Korea, Seongnam, Gyeonggi, Republic of Korea
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50
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Saletti D, Radzimanowski J, Effantin G, Midtvedt D, Mangenot S, Weissenhorn W, Bassereau P, Bally M. The Matrix protein M1 from influenza C virus induces tubular membrane invaginations in an in vitro cell membrane model. Sci Rep 2017; 7:40801. [PMID: 28120862 PMCID: PMC5264427 DOI: 10.1038/srep40801] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/12/2016] [Indexed: 02/06/2023] Open
Abstract
Matrix proteins from enveloped viruses play an important role in budding and stabilizing virus particles. In order to assess the role of the matrix protein M1 from influenza C virus (M1-C) in plasma membrane deformation, we have combined structural and in vitro reconstitution experiments with model membranes. We present the crystal structure of the N-terminal domain of M1-C and show by Small Angle X-Ray Scattering analysis that full-length M1-C folds into an elongated structure that associates laterally into ring-like or filamentous polymers. Using negatively charged giant unilamellar vesicles (GUVs), we demonstrate that M1-C full-length binds to and induces inward budding of membrane tubules with diameters that resemble the diameter of viruses. Membrane tubule formation requires the C-terminal domain of M1-C, corroborating its essential role for M1-C polymerization. Our results indicate that M1-C assembly on membranes constitutes the driving force for budding and suggest that M1-C plays a key role in facilitating viral egress.
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Affiliation(s)
- David Saletti
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
| | - Jens Radzimanowski
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000 Grenoble, France
| | - Gregory Effantin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000 Grenoble, France
| | - Daniel Midtvedt
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000 Grenoble, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
| | - Marta Bally
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
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