1
|
Schaefer A, Yang B, Schroeder HA, Harit D, Humphry MS, Zeitlin L, Whaley KJ, Ravel J, Fischer WA, Lai SK. ZMapp reduces diffusion of Ebola viral particles in fresh human cervicovaginal mucus. Emerg Microbes Infect 2024; 13:2352520. [PMID: 38713593 PMCID: PMC11100441 DOI: 10.1080/22221751.2024.2352520] [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: 12/20/2023] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Vaginal transmission from semen of male Ebola virus (EBOV) survivors has been implicated as a potential origin of Ebola virus disease (EVD) outbreaks. While EBOV in semen must traverse cervicovaginal mucus (CVM) to reach target cells, the behaviour of EBOV in CVM is poorly understood. CVM contains substantial quantities of IgG, and arrays of IgG bound to a virion can develop multiple Fc-mucin bonds, immobilizing the IgG/virion complex in mucus. Here, we measured the real-time mobility of fluorescent Ebola virus-like-particles (VLP) in 50 CVM specimens from 17 women, with and without ZMapp, a cocktail of 3 monoclonal IgGs against EBOV. ZMapp-mediated effective trapping of Ebola VLPs in CVM from a subset of women across the menstrual cycle, primarily those with Lactobacillus crispatus dominant microbiota. Our work underscores the influence of the vaginal microbiome on IgG-mucin crosslinking against EBOV and identifies bottlenecks in the sexual transmission of EBOV.
Collapse
Affiliation(s)
- Alison Schaefer
- UNC/NCSU Joint Department of Biomedical Engineering, Chapel Hill, NC, USA
| | - Bing Yang
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly A. Schroeder
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimple Harit
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mike S. Humphry
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William A. Fischer
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Chapel Hill, NC, USA
| | - Samuel K. Lai
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology & Immunology; University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
2
|
Passchier TC, White JBR, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 2024; 14:14099. [PMID: 38890308 PMCID: PMC11189427 DOI: 10.1038/s41598-024-58243-z] [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: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent Ni and Ni+1 protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the Ni+1 N-terminus and Ni-1 C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions.
Collapse
Affiliation(s)
- Tim C Passchier
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew J Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Exscientia, The Schrödinger Building Oxford Science Park, Oxford, OX4 4GE, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- College of Biomedical Sciences, Larkin University, 18301 N Miami Avenue, Miami, FL, 33169, USA.
| | - John N Barr
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
3
|
Bodmer BS, Hoenen T, Wendt L. Molecular insights into the Ebola virus life cycle. Nat Microbiol 2024; 9:1417-1426. [PMID: 38783022 DOI: 10.1038/s41564-024-01703-z] [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: 06/26/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Ebola virus and other orthoebolaviruses cause severe haemorrhagic fevers in humans, with very high case fatality rates. Their non-segmented single-stranded RNA genome encodes only seven structural proteins and a small number of non-structural proteins to facilitate the virus life cycle. The basics of this life cycle are well established, but recent advances have substantially increased our understanding of its molecular details, including the viral and host factors involved. Here we provide a comprehensive overview of our current knowledge of the molecular details of the orthoebolavirus life cycle, with a special focus on proviral host factors. We discuss the multistep entry process, viral RNA synthesis in specialized phase-separated intracellular compartments called inclusion bodies, the expression of viral proteins and ultimately the assembly of new virus particles and their release at the cell surface. In doing so, we integrate recent studies into the increasingly detailed model that has developed for these fundamental aspects of orthoebolavirus biology.
Collapse
Affiliation(s)
- Bianca S Bodmer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany.
| | - Lisa Wendt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| |
Collapse
|
4
|
Liu X, Stahelin RV, Pienaar E. Impact of Ebola virus nucleoprotein on VP40 virus-like particle production: a computational approach. Commun Biol 2024; 7:634. [PMID: 38796621 PMCID: PMC11128010 DOI: 10.1038/s42003-024-06300-8] [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: 08/15/2023] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Ebola virus (EBOV) matrix protein VP40 can assemble and bud as virus-like particles (VLPs) when expressed alone in mammalian cells. Nucleoprotein (NP) could be recruited to VLPs as inclusion body (IB) when co-expressed, and increase VLP production. However, the mechanism behind it remains unclear. Here, we use a computational approach to study NP-VP40 interactions. Our simulations indicate that NP may enhance VLP production through stabilizing VP40 filaments and accelerating the VLP budding step. Further, both the relative timing and amount of NP expression compared to VP40 are important for the effective production of IB-containing VLPs. We predict that relative NP/VP40 expression ratio and time are important for efficient production of IB-containing VLPs. We conclude that disrupting the expression timing and amount of NP and VP40 could provide new avenues to treat EBOV infection. This work provides quantitative insights into EBOV proteins interactions and how virion generation and drug efficacy could be influenced.
Collapse
Affiliation(s)
- Xiao Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
5
|
Almeida-Pinto F, Pinto R, Rocha J. Navigating the Complex Landscape of Ebola Infection Treatment: A Review of Emerging Pharmacological Approaches. Infect Dis Ther 2024; 13:21-55. [PMID: 38240994 PMCID: PMC10828234 DOI: 10.1007/s40121-023-00913-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024] Open
Abstract
In 1976 Ebola revealed itself to the world, marking the beginning of a series of localized outbreaks. However, it was the Ebola outbreak that began in 2013 that incited fear and anxiety around the globe. Since then, our comprehension of the virus has been steadily expanding. Ebola virus (EBOV), belonging to the Orthoebolavirus genus of the Filoviridae family, possesses a non-segmented, negative single-stranded RNA genome comprising seven genes that encode multiple proteins. These proteins collectively orchestrate the intricate process of infecting host cells. It is not possible to view each protein as monofunctional. Instead, they synergistically contribute to the pathogenicity of the virus. Understanding this multifaceted replication cycle is crucial for the development of effective antiviral strategies. Currently, two antibody-based therapeutics have received approval for treating Ebola virus disease (EVD). In 2022, the first evidence-based clinical practice guideline dedicated to specific therapies for EVD was published. Although notable progress has been made in recent years, deaths still occur. Consequently, there is an urgent need to enhance the therapeutic options available to improve the outcomes of the disease. Emerging therapeutics can target viral proteins as direct-acting antivirals or host factors as host-directed antivirals. They both have advantages and disadvantages. One way to bypass some disadvantages is to repurpose already approved drugs for non-EVD indications to treat EVD. This review offers detailed insight into the role of each viral protein in the replication cycle of the virus, as understanding how the virus interacts with host cells is critical to understanding how emerging therapeutics exert their activity. Using this knowledge, this review delves into the intricate mechanisms of action of current and emerging therapeutics.
Collapse
Affiliation(s)
| | - Rui Pinto
- Faculdade de Farmácia, Universidade de Lisboa, 1649-003, Lisbon, Portugal
- Laboratory of Systems Integration Pharmacology, Clinical and Regulatory Science, Research Institute for Medicines (iMED.ULisboa), 1649-003, Lisbon, Portugal
- Dr. Joaquim Chaves, Medicine Laboratory, Joaquim Chaves Saúde (JCS), Carnaxide, Portugal
| | - João Rocha
- Faculdade de Farmácia, Universidade de Lisboa, 1649-003, Lisbon, Portugal
- Laboratory of Systems Integration Pharmacology, Clinical and Regulatory Science, Research Institute for Medicines (iMED.ULisboa), 1649-003, Lisbon, Portugal
| |
Collapse
|
6
|
Sabsay KR, te Velthuis AJW. Negative and ambisense RNA virus ribonucleocapsids: more than protective armor. Microbiol Mol Biol Rev 2023; 87:e0008223. [PMID: 37750733 PMCID: PMC10732063 DOI: 10.1128/mmbr.00082-23] [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] [Indexed: 09/27/2023] Open
Abstract
SUMMARYNegative and ambisense RNA viruses are the causative agents of important human diseases such as influenza, measles, Lassa fever, and Ebola hemorrhagic fever. The viral genome of these RNA viruses consists of one or more single-stranded RNA molecules that are encapsidated by viral nucleocapsid proteins to form a ribonucleoprotein complex (RNP). This RNP acts as protection, as a scaffold for RNA folding, and as the context for viral replication and transcription by a viral RNA polymerase. However, the roles of the viral nucleoproteins extend beyond these functions during the viral infection cycle. Recent advances in structural biology techniques and analysis methods have provided new insights into the formation, function, dynamics, and evolution of negative sense virus nucleocapsid proteins, as well as the role that they play in host innate immune responses against viral infection. In this review, we discuss the various roles of nucleocapsid proteins, both in the context of RNPs and in RNA-free states, as well as the open questions that remain.
Collapse
Affiliation(s)
- Kimberly R. Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Aartjan J. W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| |
Collapse
|
7
|
Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [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: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
Collapse
Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| |
Collapse
|
8
|
Collados Rodríguez M, Maillard P, Journeaux A, Komarova AV, Najburg V, David RYS, Helynck O, Guo M, Zhong J, Baize S, Tangy F, Jacob Y, Munier-Lehmann H, Meurs EF. Novel Antiviral Molecules against Ebola Virus Infection. Int J Mol Sci 2023; 24:14791. [PMID: 37834238 PMCID: PMC10573436 DOI: 10.3390/ijms241914791] [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: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Infection with Ebola virus (EBOV) is responsible for hemorrhagic fever in humans with a high mortality rate. Combined efforts of prevention and therapeutic intervention are required to tackle highly variable RNA viruses, whose infections often lead to outbreaks. Here, we have screened the 2P2I3D chemical library using a nanoluciferase-based protein complementation assay (NPCA) and isolated two compounds that disrupt the interaction of the EBOV protein fragment VP35IID with the N-terminus of the dsRNA-binding proteins PKR and PACT, involved in IFN response and/or intrinsic immunity, respectively. The two compounds inhibited EBOV infection in cell culture as well as infection by measles virus (MV) independently of IFN induction. Consequently, we propose that the compounds are antiviral by restoring intrinsic immunity driven by PACT. Given that PACT is highly conserved across mammals, our data support further testing of the compounds in other species, as well as against other negative-sense RNA viruses.
Collapse
Affiliation(s)
- Mila Collados Rodríguez
- School of Infection & Immunity (SII), College of Medical, Veterinary and Life Sciences (MVLS), Sir Michael Stoker Building, MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Patrick Maillard
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Alexandra Journeaux
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France;
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Raul-Yusef Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Blizard Institute—Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Olivier Helynck
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Mingzhe Guo
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Jin Zhong
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Sylvain Baize
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Yves Jacob
- Université Paris Cité, 75013 Paris, France;
- Unité Génétique Moléculaire des Virus à ARN, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France
| | - Hélène Munier-Lehmann
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Eliane F. Meurs
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| |
Collapse
|
9
|
Narkhede YB, Bhardwaj A, Motsa BB, Saxena R, Sharma T, Chapagain PP, Stahelin RV, Wiest O. Elucidating Residue-Level Determinants Affecting Dimerization of Ebola Virus Matrix Protein Using High-Throughput Site Saturation Mutagenesis and Biophysical Approaches. J Phys Chem B 2023; 127:6449-6461. [PMID: 37458567 DOI: 10.1021/acs.jpcb.3c01759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The Ebola virus (EBOV) is a filamentous virus that acquires its lipid envelope from the plasma membrane of the host cell it infects. EBOV assembly and budding from the host cell plasma membrane are mediated by a peripheral protein, known as the matrix protein VP40. VP40 is a 326 amino acid protein with two domains that are loosely linked. The VP40 N-terminal domain (NTD) contains a hydrophobic α-helix, which mediates VP40 dimerization. The VP40 C-terminal domain has a cationic patch, which mediates interactions with anionic lipids and a hydrophobic region that mediates VP40 dimer-dimer interactions. The VP40 dimer is necessary for trafficking to the plasma membrane inner leaflet and interactions with anionic lipids to mediate the VP40 assembly and oligomerization. Despite significant structural information available on the VP40 dimer structure, little is known on how the VP40 dimer is stabilized and how residues outside the NTD hydrophobic portion of the α-helical dimer interface contribute to dimer stability. To better understand how VP40 dimer stability is maintained, we performed computational studies using per-residue energy decomposition and site saturation mutagenesis. These studies revealed a number of novel keystone residues for VP40 dimer stability just adjacent to the α-helical dimer interface as well as distant residues in the VP40 CTD that can stabilize the VP40 dimer form. Experimental studies with representative VP40 mutants in vitro and in cells were performed to test computational predictions that reveal residues that alter VP40 dimer stability. Taken together, these studies provide important biophysical insights into VP40 dimerization and may be useful in strategies to weaken or alter the VP40 dimer structure as a means of inhibiting the EBOV assembly.
Collapse
Affiliation(s)
- Yogesh B Narkhede
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Atul Bhardwaj
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Balindile B Motsa
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Roopashi Saxena
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | | | | | - Robert V Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
10
|
Fang J, Castillon G, Phan S, McArdle S, Hariharan C, Adams A, Ellisman MH, Deniz AA, Saphire EO. Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories. Nat Commun 2023; 14:4159. [PMID: 37443171 PMCID: PMC10345124 DOI: 10.1038/s41467-023-39821-7] [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: 12/21/2022] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather and coordinate viral transcription, replication, and assembly. Key to viral factory function is the recruitment of EBOV polymerase, a multifunctional machine that mediates transcription and replication of the viral RNA genome. We show that intracellularly reconstituted EBOV viral factories are biomolecular condensates, with composition-dependent internal exchange dynamics that likely facilitates viral replication. Within the viral factory, we found the EBOV polymerase clusters into foci. The distance between these foci increases when viral replication is enabled. In addition to the typical droplet-like viral factories, we report the formation of network-like viral factories during EBOV infection. Unlike droplet-like viral factories, network-like factories are inactive for EBOV nucleocapsid assembly. This unique view of EBOV propagation suggests a form-to-function relationship that describes how physical properties and internal structures of biomolecular condensates influence viral biogenesis.
Collapse
Affiliation(s)
- Jingru Fang
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Scripps Research, La Jolla, CA, USA
| | - Guillaume Castillon
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sara McArdle
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Aiyana Adams
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | | | | |
Collapse
|
11
|
Saeki K, Sasaki A. Cell-to-cell transmission promotes the emergence of double-drug resistance. Virus Evol 2023; 9:vead017. [PMID: 37744652 PMCID: PMC10517696 DOI: 10.1093/ve/vead017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/08/2023] [Indexed: 09/26/2023] Open
Abstract
The use of multiple antivirals in a single patient increases the risk of emergence of multidrug-resistant viruses, posing a public health challenge and limiting management options. Cell-to-cell viral transmission allows a pair of viruses that are each resistant to a single drug to persist for a prolonged period of passages although neither can survive alone under double-drug treatment. This pair should then persist until they accumulate a second mutation to generate resistance to both drugs. Accordingly, we here propose a hypothesis that viruses have a much higher probability of developing double-drug resistance when they are transmitted via a cell-to-cell mode than when they are transmitted via a cell-free mode through released virions. By using a stochastic model describing the changes in the frequencies of viral genotypes over successive infections, we analytically demonstrate that the emergence probability of double resistance is approximately the square of the number of viral genomes that establish infection times greater in cell-to-cell transmission than in cell-free transmission. Our study suggests the importance of inhibiting cell-to-cell transmission during multidrug treatment.
Collapse
Affiliation(s)
- Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School for Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Akira Sasaki
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa 240-0193, Japan
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg A-2361, Austria
| |
Collapse
|
12
|
Shirogane Y, Harada H, Hirai Y, Takemoto R, Suzuki T, Hashiguchi T, Yanagi Y. Collective fusion activity determines neurotropism of an en bloc transmitted enveloped virus. SCIENCE ADVANCES 2023; 9:eadf3731. [PMID: 36706187 PMCID: PMC9882980 DOI: 10.1126/sciadv.adf3731] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/29/2022] [Indexed: 06/09/2023]
Abstract
Measles virus (MeV), which is usually non-neurotropic, sometimes persists in the brain and causes subacute sclerosing panencephalitis (SSPE) several years after acute infection, serving as a model for persistent viral infections. The persisting MeVs have hyperfusogenic mutant fusion (F) proteins that likely enable cell-cell fusion at synapses and "en bloc transmission" between neurons. We here show that during persistence, F protein fusogenicity is generally enhanced by cumulative mutations, yet mutations paradoxically reducing the fusogenicity may be selected alongside the wild-type (non-neurotropic) MeV genome. A mutant F protein having SSPE-derived substitutions exhibits lower fusogenicity than the hyperfusogenic F protein containing some of those substitutions, but by the wild-type F protein coexpression, the fusogenicity of the former F protein is enhanced, while that of the latter is nearly abolished. These findings advance the understanding of the long-term process of MeV neuropathogenicity and provide critical insight into the genotype-phenotype relationships of en bloc transmitted viruses.
Collapse
Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Hidetaka Harada
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Yuichi Hirai
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ryuichi Takemoto
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Yanagi
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
13
|
Popovic M. Why doesn't Ebola virus cause pandemics like SARS-CoV-2? MICROBIAL RISK ANALYSIS 2022; 22:100236. [PMID: 36312211 PMCID: PMC9597532 DOI: 10.1016/j.mran.2022.100236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/22/2022] [Indexed: 06/01/2023]
Abstract
Ebola virus is among the most dangerous, contagious and deadly etiological causes of viral diseases. However, Ebola virus has never extensively spread in human population and never have led to a pandemic. Why? The mechanistic biophysical model revealing the biothermodynamic background of virus-host interaction) could help us to understand pathogenesis of Ebola virus disease (earlier known as the Ebola hemorrhagic fever). In this paper for the first time the empirical formula, thermodynamic properties of biosynthesis (including the driving force of virus multiplication in the susceptible host), binding constant and thermodynamic properties of binding are reported. Thermodynamic data for Ebola virus were compared with data for SARS-CoV-2 to explain why SARS-CoV-2 has caused a pandemic, while Ebola remains on local epidemic level. The empirical formula of the Ebola virus was found to be CH1.569O0.3281N0.2786P0.00173S0.00258. Standard Gibbs energy of biosynthesis of the Ebola virus nucleocapsid is -151.59 kJ/C-mol.
Collapse
Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
14
|
Segredo-Otero E, Sanjuán R. Cooperative Virus-Virus Interactions: An Evolutionary Perspective. BIODESIGN RESEARCH 2022; 2022:9819272. [PMID: 37850129 PMCID: PMC10521650 DOI: 10.34133/2022/9819272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/21/2022] [Indexed: 10/19/2023] Open
Abstract
Despite extensive evidence of virus-virus interactions, not much is known about their biological significance. Importantly, virus-virus interactions could have evolved as a form of cooperation or simply be a by-product of other processes. Here, we review and discuss different types of virus-virus interactions from the point of view of social evolution, which provides a well-established framework for interpreting the fitness costs and benefits of such traits. We also classify interactions according to their mechanisms of action and speculate on their evolutionary implications. As in any other biological system, the evolutionary stability of viral cooperation critically requires cheaters to be excluded from cooperative interactions. We discuss how cheater viruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.
Collapse
Affiliation(s)
- Ernesto Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| |
Collapse
|
15
|
Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
Collapse
Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| |
Collapse
|
16
|
Abstract
Filovirus-infected cells are characterized by typical cytoplasmic inclusion bodies (IBs) located in the perinuclear region. The formation of these IBs is induced mainly by the accumulation of the filoviral nucleoprotein NP, which recruits the other nucleocapsid proteins, the polymerase co-factor VP35, the polymerase L, the transcription factor VP30 and VP24 via direct or indirect protein-protein interactions. Replication of the negative-strand RNA genomes by the viral polymerase L and VP35 occurs in the IBs, resulting in the synthesis of positive-strand genomes, which are encapsidated by NP, thus forming ribonucleoprotein complexes (antigenomic RNPs). These newly formed antigenomic RNPs in turn serve as templates for the synthesis of negative-strand RNA genomes that are also encapsidated by NP (genomic RNPs). Still in the IBs, genomic RNPs mature into tightly packed transport-competent nucleocapsids (NCs) by the recruitment of the viral protein VP24. NCs are tightly coiled left-handed helices whose structure is mainly determined by the multimerization of NP at its N-terminus, and these helices form the inner layer of the NCs. The RNA genome is fixed by 2 lobes of the NP N-terminus and is thus guided by individual NP molecules along the turns of the helix. Direct interaction of the NP C-terminus with the VP35 and VP24 molecules forms the outer layer of the NCs. Once formed, NCs that are located at the border of the IBs recruit actin polymerization machinery to one of their ends to drive their transport to budding sites for their envelopment and final release. Here, we review the current knowledge on the structure, assembly, and transport of filovirus NCs.
Collapse
Affiliation(s)
- Olga Dolnik
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
17
|
Liu X, Pappas EJ, Husby ML, Motsa BB, Stahelin RV, Pienaar E. Mechanisms of phosphatidylserine influence on viral production: A computational model of Ebola virus matrix protein assembly. J Biol Chem 2022; 298:102025. [PMID: 35568195 PMCID: PMC9218153 DOI: 10.1016/j.jbc.2022.102025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Ebola virus (EBOV) infections continue to pose a global public health threat, with high mortality rates and sporadic outbreaks in Central and Western Africa. A quantitative understanding of the key processes driving EBOV assembly and budding could provide valuable insights to inform drug development. Here, we use a computational model to evaluate EBOV matrix assembly. Our model focuses on the assembly kinetics of VP40, the matrix protein in EBOV, and its interaction with phosphatidylserine (PS) in the host cell membrane. It has been shown that mammalian cells transfected with VP40-expressing plasmids are capable of producing virus-like particles (VLPs) that closely resemble EBOV virions. Previous studies have also shown that PS levels in the host cell membrane affects VP40 association with the plasma membrane inner leaflet and that lower membrane PS levels result in lower VLP production. Our computational findings indicate that PS may also have a direct influence on VP40 VLP assembly and budding, where a higher PS level will result in a higher VLP budding rate and filament dissociation rate. Our results further suggest that the assembly of VP40 filaments follow the nucleation-elongation theory, where initialization and oligomerization of VP40 are two distinct steps in the assembly process. Our findings advance the current understanding of VP40 VLP formation by identifying new possible mechanisms of PS influence on VP40 assembly. We propose that these mechanisms could inform treatment strategies targeting PS alone or in combination with other VP40 assembly steps.
Collapse
Affiliation(s)
- Xiao Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ethan J Pappas
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Monica L Husby
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Balindile B Motsa
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA.
| |
Collapse
|
18
|
A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations. Microbiol Mol Biol Rev 2022; 86:e0008621. [PMID: 35658541 DOI: 10.1128/mmbr.00086-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.
Collapse
|
19
|
A point mutation in human parainfluenza virus type 2 nucleoprotein leads to two separate effects on virus replication. J Virol 2021; 96:e0206721. [PMID: 34878809 DOI: 10.1128/jvi.02067-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paramyxovirus genomes, like that of human parainfluenza virus type 2 (hPIV2), are precisely a multiple of six nucleotides long ("rule of six"), in which each nucleoprotein subunit (NP) binds precisely 6 nucleotides. Ten residues of its RNA binding groove contact the genome RNA; but only one, Q202, directly contacts a nucleotide base. Mutation of NPQ202 leads to two phenotypes; the ability of the viral polymerase to replicate minigenomes with defective bipartite promoters where NPwt is inactive, and the inability to rescue rPIV2 carrying this point mutation by standard means. The absence a rPIV2 NPQ202A prevented further study of this latter phenotype. By extensive and repeated co-cultivation of transfected cells, a rPIV2 carrying this mutation was finally recovered, and this virus was apparently viable due to the presence of an additional NP mutation (I35L). Our results suggest that these two phenotypes are due to separate effects of the Q202 mutation, and that of the problematic rescue phenotype may be due to the inability of the transfected cell to incorporate viral nucleocapsids during virus budding. Importance Paramyxovirus genomes are contained within a non-covalent homopolymer of its nucleoprotein (NP) and form helical nucleocapsids (NC) whose 3' ends contain the promoters for the initiation of viral RNA synthesis. This work suggests that these NC 3' ends may play another role in the virus life cycle, namely via their specific interaction with virus modified cell membranes needed for the incorporation of viral NCs into budding virions.
Collapse
|
20
|
Banerjee G, Shokeen K, Chakraborty N, Agarwal S, Mitra A, Kumar S, Banerjee P. Modulation of immune response in Ebola virus disease. Curr Opin Pharmacol 2021; 60:158-167. [PMID: 34425392 DOI: 10.1016/j.coph.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Ebola virus disease targets and destroys immune cells, including macrophages and dendritic cells, leading to impairment of host response. After infection, a combination of strategies including alteration and evasion of immune response culminating in a strong inflammatory response can lead to multi-organ failure and death in most infected patients. This review discusses immune response dynamics, mainly focusing on how Ebola manipulates innate and adaptive immune responses and strategizes to thwart host immune responses. We also discuss the challenges and prospects of developing therapeutics and vaccines against Ebola.
Collapse
Affiliation(s)
- Goutam Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kamal Shokeen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Nilanjan Chakraborty
- Department of Microbiology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Saumya Agarwal
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Arindam Mitra
- Department of Microbiology, Adamas University, Kolkata, West Bengal, 700126, India.
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
21
|
Identification and Characterization of Defective Viral Genomes in Ebola Virus-Infected Rhesus Macaques. J Virol 2021; 95:e0071421. [PMID: 34160256 DOI: 10.1128/jvi.00714-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebola virus (EBOV), of the family Filoviridae, is an RNA virus that can cause a hemorrhagic fever with a high mortality rate. Defective viral genomes (DVGs) are truncated genomes that have been observed during multiple RNA virus infections, including in vitro EBOV infection, and have previously been associated with viral persistence and immunostimulatory activity. As DVGs have been detected in cells persistently infected with EBOV, we hypothesized that DVGs may also accumulate during viral replication in filovirus-infected hosts. Therefore, we interrogated sequence data from serum and tissue samples using a bioinformatics tool in order to identify the presence of DVGs in nonhuman primates (NHPs) infected with EBOV, Sudan virus (SUDV), or Marburg virus (MARV). Multiple 5' copy-back DVGs (cbDVGs) were detected in NHP serum during the acute phase of filovirus infection. While the relative abundance of total DVGs in most animals was low, serum collected during acute EBOV and SUDV infections, but not MARV infections, contained a higher proportion of short trailer sequence cbDVGs than the challenge stock. This indicated an accumulation of these DVGs throughout infection, potentially due to the preferential replication of short DVGs over the longer viral genome. Using reverse transcriptase PCR (RT-PCR) and deep sequencing, we also confirmed the presence of 5' cbDVGs in EBOV-infected NHP testes, which is of interest due to EBOV persistence in semen of male survivors of infection. This work suggests that DVGs play a role in EBOV infection in vivo and that further study will lead to a better understanding of EBOV pathogenesis. IMPORTANCE The study of filovirus pathogenesis is critical for understanding the consequences of infection and for the development of strategies to ameliorate future outbreaks. Defective viral genomes (DVGs) have been detected during EBOV infections in vitro; however, their presence in in vivo infections remains unknown. In this study, DVGs were detected in samples collected from EBOV- and SUDV-infected nonhuman primates (NHPs). The accumulation of these DVGs in the trailer region of the genome during infection indicates a potential role in EBOV and SUDV pathogenesis. In particular, the presence of DVGs in the testes of infected NHPs requires further investigation as it may be linked to the establishment of persistence.
Collapse
|
22
|
Ghosh S, Saha A, Samanta S, Saha RP. Genome structure and genetic diversity in the Ebola virus. Curr Opin Pharmacol 2021; 60:83-90. [PMID: 34364102 DOI: 10.1016/j.coph.2021.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022]
Abstract
Ebola is a deadly pathogen responsible for Ebola virus disease, first came to prominence in the year 1976. This rapidly evolving virus imposed a serious threat to the human population in the last few decades and also continues to be a probable threat to our race. A better understanding of the virus in terms of its genomic structure is very much needed to develop an effective antiviral therapy against this deadly pathogen. Complete knowledge of its genomic structure and variations will help us and the entire scientific community to design effective therapy in terms of either vaccine development or the development of proper antiviral medicine.
Collapse
Affiliation(s)
- Sanmitra Ghosh
- Department of Microbiology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Rudra P Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India.
| |
Collapse
|
23
|
DiCecco LA, D'Elia A, Miller C, Sask KN, Soleymani L, Grandfield K. Electron Microscopy Imaging Applications of Room Temperature Ionic Liquids in the Biological Field: A Review. Chembiochem 2021; 22:2488-2506. [PMID: 33690961 DOI: 10.1002/cbic.202100041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/08/2021] [Indexed: 11/11/2022]
Abstract
For biological imaging using electron microscopy (EM), the use of room-temperature ionic liquids (RTILs) has been proposed as an alternative to traditional lengthy preparation methods. With their low vapor pressures and conductivity, RTILs can be applied onto hard-to-image soft and/or wet samples without dehydration - allowing for a more representative, hydrated state of material and opening the possibility for visualization of in situ physiological processes using conventional EM systems. However, RTILs have yet to be utilized to their full potential by microscopists and microbiologists alike. To this end, this review aims to provide a comprehensive summary of biological applications of RTILs for EM to bridge the RTIL, in situ microscopy, and biological communities. We outline future research avenues for the use of RTILs for the EM observation of biological samples, notably i) RTIL selection and optimization, ii) applications for live cell processes and iii) electron beam and ionic liquid interaction studies.
Collapse
Affiliation(s)
- Liza-Anastasia DiCecco
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| | - Andrew D'Elia
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| | - Chelsea Miller
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| | - Kyla N Sask
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| | - Kathryn Grandfield
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L7, Canada
| |
Collapse
|
24
|
Abstract
Despite their simplicity, viruses exhibit certain types of social interactions. Situations in which a given virus achieves higher fitness in combination with other members of the viral population have been described at the level of transmission, replication, suppression of host immune responses, and host killing, enabling the evolution of viral cooperation. Although cellular coinfection with multiple viral particles is the typical playground for these interactions, cooperation between viruses infecting different cells is also established through cellular and viral-encoded communication systems. In general, the stability of cooperation is compromised by cheater genotypes, as best exemplified by defective interfering particles. As predicted by social evolution theory, cheater invasion can be avoided when cooperators interact preferentially with other cooperators, a situation that is promoted in spatially structured populations. Processes such as transmission bottlenecks, organ compartmentalization, localized spread of infection foci, superinfection exclusion, and even discrete intracellular replication centers promote multilevel spatial structuring in viruses. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas and Universitat de València, 46980 Paterna, València, Spain;
| |
Collapse
|
25
|
Zhang N, Shan H, Liu M, Li T, Luo R, Yang L, Qi L, Chu X, Su X, Wang R, Liu Y, Sun W, Shen QT. Structure and assembly of double-headed Sendai virus nucleocapsids. Commun Biol 2021; 4:494. [PMID: 33888861 PMCID: PMC8062630 DOI: 10.1038/s42003-021-02027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/23/2021] [Indexed: 01/17/2023] Open
Abstract
Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.
Collapse
Affiliation(s)
- Na Zhang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Shan
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mingdong Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianhao Li
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaofeng Chu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Su
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Wang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunhui Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qing-Tao Shen
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| |
Collapse
|
26
|
de la Fuente IF, Sawant SS, Tolentino MQ, Corrigan PM, Rouge JL. Viral Mimicry as a Design Template for Nucleic Acid Nanocarriers. Front Chem 2021; 9:613209. [PMID: 33777893 PMCID: PMC7987652 DOI: 10.3389/fchem.2021.613209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Therapeutic nucleic acids hold immense potential in combating undruggable, gene-based diseases owing to their high programmability and relative ease of synthesis. While the delivery of this class of therapeutics has successfully entered the clinical setting, extrahepatic targeting, endosomal escape efficiency, and subcellular localization. On the other hand, viruses serve as natural carriers of nucleic acids and have acquired a plethora of structures and mechanisms that confer remarkable transfection efficiency. Thus, understanding the structure and mechanism of viruses can guide the design of synthetic nucleic acid vectors. This review revisits relevant structural and mechanistic features of viruses as design considerations for efficient nucleic acid delivery systems. This article explores how viral ligand display and a metastable structure are central to the molecular mechanisms of attachment, entry, and viral genome release. For comparison, accounted for are details on the design and intracellular fate of existing nucleic acid carriers and nanostructures that share similar and essential features to viruses. The review, thus, highlights unifying themes of viruses and nucleic acid delivery systems such as genome protection, target specificity, and controlled release. Sophisticated viral mechanisms that are yet to be exploited in oligonucleotide delivery are also identified as they could further the development of next-generation nonviral nucleic acid vectors.
Collapse
Affiliation(s)
| | | | | | | | - Jessica L. Rouge
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| |
Collapse
|
27
|
Misasi J, Sullivan NJ. Immunotherapeutic strategies to target vulnerabilities in the Ebolavirus glycoprotein. Immunity 2021; 54:412-436. [PMID: 33691133 DOI: 10.1016/j.immuni.2021.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
The 2014 Ebola virus disease (EVD) outbreak in West Africa and the subsequent outbreaks of 2018-2020 in Equator and North Kivu provinces of the Democratic Republic of the Congo illustrate the public health challenges of emerging and reemerging viruses. EVD has a high case fatality rate with a rapidly progressing syndrome of fever, rash, vomiting, diarrhea, and bleeding diathesis. Recently, two monoclonal-antibody-based therapies received United States Food and Drug Administration (FDA) approval, and there are several other passive immunotherapies that hold promise as therapeutics against other species of Ebolavirus. Here, we review concepts needed to understand mechanisms of action, present an expanded schema to define additional sites of vulnerability on the viral glycoprotein, and review current antibody-based therapeutics. The concepts described are used to gain insights into the key characteristics that represent functional targets for immunotherapies against Zaire Ebolavirus and other emerging viruses within the Ebolavirus genus.
Collapse
Affiliation(s)
- John Misasi
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
28
|
Yoon BK, Jeon WY, Sut TN, Cho NJ, Jackman JA. Stopping Membrane-Enveloped Viruses with Nanotechnology Strategies: Toward Antiviral Drug Development and Pandemic Preparedness. ACS NANO 2021; 15:125-148. [PMID: 33306354 DOI: 10.1021/acsnano.0c07489] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Membrane-enveloped viruses are a leading cause of viral epidemics, and there is an outstanding need to develop broad-spectrum antiviral strategies to treat and prevent enveloped virus infections. In this review, we critically discuss why the lipid membrane surrounding enveloped virus particles is a promising antiviral target and cover the latest progress in nanotechnology research to design and evaluate membrane-targeting virus inhibition strategies. These efforts span diverse topics such as nanomaterials, self-assembly, biosensors, nanomedicine, drug delivery, and medical devices and have excellent potential to support the development of next-generation antiviral drug candidates and technologies. Application examples in the areas of human medicine and agricultural biosecurity are also presented. Looking forward, research in this direction is poised to strengthen capabilities for virus pandemic preparedness and demonstrates how nanotechnology strategies can help to solve global health challenges related to infectious diseases.
Collapse
Affiliation(s)
- Bo Kyeong Yoon
- School of Chemical Engineering and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Won-Yong Jeon
- School of Chemical Engineering and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Tun Naw Sut
- School of Chemical Engineering and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Joshua A Jackman
- School of Chemical Engineering and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
29
|
Barfoot S, Poger D, Mark AE. Understanding the Activated Form of a Class-I Fusion Protein: Modeling the Interaction of the Ebola Virus Glycoprotein 2 with a Lipid Bilayer. Biochemistry 2020; 59:4051-4058. [PMID: 32960042 DOI: 10.1021/acs.biochem.0c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fusion of the viral and target cell membranes is a key step in the life cycle of all enveloped viruses. Here, a range of structural data is used to generate an evidence-based model of the active conformation of an archetypical type-I fusion protein, the Ebola glycoprotein 2 (GP2). The stability of the trimeric complex is demonstrated using molecular dynamics and validated by simulating the interaction of the complex with a lipid bilayer. In this model, the fusion peptides project away from the central helix bundle parallel to the target membrane. This maximizes contact with the host membrane, enhances lateral stability, and would explain why, when activated, viral fusion proteins are trimeric.
Collapse
Affiliation(s)
- Shelley Barfoot
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Poger
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| |
Collapse
|
30
|
Wan W, Clarke M, Norris MJ, Kolesnikova L, Koehler A, Bornholdt ZA, Becker S, Saphire EO, Briggs JA. Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers. eLife 2020; 9:59225. [PMID: 33016878 PMCID: PMC7588233 DOI: 10.7554/elife.59225] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/02/2020] [Indexed: 01/28/2023] Open
Abstract
Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and generation of membrane curvature are intrinsic properties of VP40. There has been no direct information on the structure of VP40 matrix layers within viruses or virus-like particles. We present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, and within intact Marburg viruses. VP40 dimers assemble extended chains via C-terminal domain interactions. These chains stack to form 2D matrix lattices below the membrane surface. These lattices form a patchwork assembly across the membrane and suggesting that assembly may begin at multiple points. Our observations define the structure and arrangement of the matrix protein layer that mediates formation of filovirus particles.
Collapse
Affiliation(s)
- William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mairi Clarke
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael J Norris
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, United States
| | - Larissa Kolesnikova
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Alexander Koehler
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | | | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, United States
| | - John Ag Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
31
|
Cooper L, Schafer A, Li Y, Cheng H, Medegan Fagla B, Shen Z, Nowar R, Dye K, Anantpadma M, Davey RA, Thatcher GRJ, Rong L, Xiong R. Screening and Reverse-Engineering of Estrogen Receptor Ligands as Potent Pan-Filovirus Inhibitors. J Med Chem 2020; 63:11085-11099. [PMID: 32886512 DOI: 10.1021/acs.jmedchem.0c01001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Filoviridae, including Ebola (EBOV) and Marburg (MARV) viruses, are emerging pathogens that pose a serious threat to public health. No agents have been approved to treat filovirus infections, representing a major unmet medical need. The selective estrogen receptor modulator (SERM) toremifene was previously identified from a screen of FDA-approved drugs as a potent EBOV viral entry inhibitor, via binding to EBOV glycoprotein (GP). A focused screen of ER ligands identified ridaifen-B as a potent dual inhibitor of EBOV and MARV. Optimization and reverse-engineering to remove ER activity led to a novel compound 30 (XL-147) showing potent inhibition against infectious EBOV Zaire (0.09 μM) and MARV (0.64 μM). Mutagenesis studies confirmed that inhibition of EBOV viral entry is mediated by the direct interaction with GP. Importantly, compound 30 displayed a broad-spectrum antifilovirus activity against Bundibugyo, Tai Forest, Reston, and Měnglà viruses and is the first submicromolar antiviral agent reported for some of these strains, therefore warranting further development as a pan-filovirus inhibitor.
Collapse
Affiliation(s)
- Laura Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Adam Schafer
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Yangfeng Li
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Bani Medegan Fagla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Zhengnan Shen
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Raghad Nowar
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Katherine Dye
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Manu Anantpadma
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, Boston, Massachusetts 02118, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Robert A Davey
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, Boston, Massachusetts 02118, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Gregory R J Thatcher
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rui Xiong
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| |
Collapse
|
32
|
Gale P. How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV. MICROBIAL RISK ANALYSIS 2020; 15:100104. [PMID: 32292808 PMCID: PMC7110232 DOI: 10.1016/j.mran.2020.100104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 05/14/2023]
Abstract
Virus binding to host cells involves specific interactions between viral (glyco)proteins (GP) and host cell surface receptors (Cr) (protein or sialic acid (SA)). The magnitude of the enthalpy of association changes with temperature according to the change in heat capacity (ΔCp) on GP/Cr binding, being little affected for avian influenza virus (AIV) haemagglutinin (HA) binding to SA (ΔCp = 0 kJ/mol/K) but greatly affected for HIV gp120 binding to CD4 receptor (ΔCp = -5.0 kJ/mol/K). A thermodynamic model developed here predicts that values of ΔCp from 0 to ~-2.0 kJ/mol/K have relatively little impact on the temperature sensitivity of the number of mosquito midgut cells with bound arbovirus, while intermediate values of ΔCp of ~-3.0 kJ/mol/K give a peak binding at a temperature of ~20 °C as observed experimentally for Western equine encephalitis virus. More negative values of ΔCp greatly decrease arbovirus binding at temperatures below ~20 °C. Thus to promote transmission at low temperatures, arboviruses may benefit from ΔCp ~ 0 kJ/mol/K as for HA/SA and it is interesting that bluetongue virus binds to SA in midge midguts. Large negative values of ΔCp as for HIV gp120:CD4 diminish binding at 37 °C. Of greater importance, however, is the decrease in entropy of the whole virus (ΔSa_immob) on its immobilisation on the host cell surface. ΔSa_immob presents a repulsive force which the enthalpy-driven GP/Cr interactions weakened at higher temperatures struggle to overcome. ΔSa_immob is more negative (less favourable) for larger diameter viruses which therefore show diminished binding at higher temperatures than smaller viruses. It is proposed that small size phenotype through a less negative ΔSa_immob is selected for viruses infecting warmer hosts thus explaining the observation that virion volume decreases with increasing host temperature from 0 °C to 40 °C in the case of dsDNA viruses. Compared to arboviruses which also infect warm-blooded vertebrates, HIV is large at 134 nm diameter and thus would have a large negative ΔSa_immob which would diminish its binding at human body temperature. It is proposed that prior non-specific binding of HIV through attachment factors takes much of the entropy loss for ΔSa_immob so enhancing subsequent specific gp120:CD4 binding at 37 °C. This is consistent with the observation that HIV attachment factors are not essential but augment infection. Antiviral therapies should focus on increasing virion size, for example through binding of zinc oxide nanoparticles to herpes simplex virus, hence making ΔSa_immob more negative, and thus reducing binding affinity at 37 °C.
Collapse
Key Words
- AIV, avian influenza virus
- Antivirals
- BBF, brush border fragments from midgut
- BTV, bluetongue virus
- C.VT, number of host cells with bound virus at temperature T
- CD4, host cell receptor for HIV
- Cp, heat capacity at constant pressure
- Cr, host cell receptor
- Ctotal, number of host cells which can bind virus in a given volume of host fluid (midgut or blood)
- DENV, Dengue virus
- EA, activation energy
- EBOV, Zaire ebolavirus
- EM, electron microscopy
- Entropy
- Env, HIV gp120 trimer envelope protein which binds to a single CD4 molecule
- FcT, fraction of arthropod midgut cells with bound virus at temperature T
- GP, viral (glyco)protein on virus surface that binds to Cr
- HA, haemagglutinin
- HIV, human immunodeficiency virus
- HSV-2, herpes simplex virus type 2
- Heat capacity
- Ka_virus_T, association constant for binding of virus to host cells at temperature T
- Kd_receptor_T, dissociation constant for GP from Cr at temperature T
- Kd_virus, dissociation constant for virus from host cell
- M, molar (moles dm-3)
- R, ideal gas constant
- SA, sialic acid
- SIV, simian immunodeficiency virus
- Temperature
- Vfree, virus not bound to cells
- Virus size
- Vtotal, virus challenge dose in volume of host fluid
- WEEV, Western equine encephalitis virus
- WNV, West Nile virus
- ZnOT, zinc oxide tetrapod
- n, number of GP/Cr contacts made on virus binding to cell
- pcompleteT, probability given a virion has bound to the surface of a midgut cell that that midgut cell becomes infected and that its progeny viruses go on to infect the salivary gland so completing the arthropod infection process within the life time of the arthropod at temperature T
- ptransmissionT, probability of successful infection of the arthropod salivary glands after oral exposure at temperature T
- ΔCp, change in heat capacity
- ΔGa_virus_T, change in Gibbs free energy on association of virus and host cell at temperature T
- ΔHa_receptor_T, change in enthalpy for binding of virus GP to host Cr receptor at a temperature T
- ΔHa_virus_T, change in enthalpy for binding of virus to host cell at temperature T
- ΔSa_immob, change in entropy on immobilization of whole virus to cell surface
- ΔSa_non_specific, change in entropy on immobilization of virus to cell surface through non-specific binding
- ΔSa_receptor_T, change in entropy for binding of virus GP to host Cr receptor
- ΔSa_specific, change in entropy on immobilization of virus to cell surface through specific GP/Cr-driven binding
- ΔSa_virus_T, change in entropy for binding of virus to host cell at temperature T
Collapse
Affiliation(s)
- Paul Gale
- Independent Scientist, 15 Weare Close, Portland, Dorset, DT5 1JP, United Kingdom
| |
Collapse
|
33
|
Zottig X, Côté-Cyr M, Arpin D, Archambault D, Bourgault S. Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1008. [PMID: 32466176 PMCID: PMC7281494 DOI: 10.3390/nano10051008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022]
Abstract
Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.
Collapse
Affiliation(s)
- Ximena Zottig
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mélanie Côté-Cyr
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Dominic Arpin
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Denis Archambault
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC H2L 2C4, Canada; (X.Z.); (M.C.-C.); (D.A.)
- The Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec, QC G1V 0A6, Canada
- The Swine and Poultry Infectious Diseases Research Centre, CRIPA, Saint-Hyacinthe, QC J2S 2M2, Canada
| |
Collapse
|
34
|
Yurdakul C, Avci O, Matlock A, Devaux AJ, Quintero MV, Ozbay E, Davey RA, Connor JH, Karl WC, Tian L, Ünlü MS. High-Throughput, High-Resolution Interferometric Light Microscopy of Biological Nanoparticles. ACS NANO 2020; 14:2002-2013. [PMID: 32003974 DOI: 10.1021/acsnano.9b08512] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Label-free, visible light microscopy is an indispensable tool for studying biological nanoparticles (BNPs). However, conventional imaging techniques have two major challenges: (i) weak contrast due to low-refractive-index difference with the surrounding medium and exceptionally small size and (ii) limited spatial resolution. Advances in interferometric microscopy have overcome the weak contrast limitation and enabled direct detection of BNPs, yet lateral resolution remains as a challenge in studying BNP morphology. Here, we introduce a wide-field interferometric microscopy technique augmented by computational imaging to demonstrate a 2-fold lateral resolution improvement over a large field-of-view (>100 × 100 μm2), enabling simultaneous imaging of more than 104 BNPs at a resolution of ∼150 nm without any labels or sample preparation. We present a rigorous vectorial-optics-based forward model establishing the relationship between the intensity images captured under partially coherent asymmetric illumination and the complex permittivity distribution of nanoparticles. We demonstrate high-throughput morphological visualization of a diverse population of Ebola virus-like particles and a structurally distinct Ebola vaccine candidate. Our approach offers a low-cost and robust label-free imaging platform for high-throughput and high-resolution characterization of a broad size range of BNPs.
Collapse
Affiliation(s)
- Celalettin Yurdakul
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Oguzhan Avci
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alex Matlock
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alexander J Devaux
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Maritza V Quintero
- Department of Biochemistry and Structural Biology , University of Texas Health San Antonio , San Antonio , Texas 78229 , United States
| | - Ekmel Ozbay
- Department of Electrical and Electronics Engineering , Bilkent University , 06800 Ankara , Turkey
| | - Robert A Davey
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - W Clem Karl
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Lei Tian
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| |
Collapse
|
35
|
Andreu-Moreno I, Sanjuán R. Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles. mBio 2020; 11:e02156-19. [PMID: 31911487 PMCID: PMC6946798 DOI: 10.1128/mbio.02156-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/18/2019] [Indexed: 01/30/2023] Open
Abstract
A growing number of studies report that viruses can spread in groups in so-called collective infectious units. By increasing the cellular multiplicity of infection, collective dispersal may allow for social-like interactions, such as cooperation or cheating. Yet, little is known about how such interactions evolve. In previous work with vesicular stomatitis virus, we showed that virion aggregation accelerates early infection stages in most cell types, providing a short-term fitness benefit to the virus. Here, we examine the effects of virion aggregation over several infection cycles. Flow cytometry, deep sequencing, infectivity assays, reverse transcription-quantitative PCR, and electron microscopy revealed that virion aggregation rapidly promotes the emergence of defective interfering particles. Therefore, virion aggregation provides immediate fitness benefits to the virus but incurs fitness costs after a few viral generations. This suggests that an optimal strategy for the virus is to undergo virion aggregation only episodically, for instance, during interhost transmission.IMPORTANCE Recent insights have revealed that viruses use a highly diverse set of strategies to release multiple viral genomes into the same target cells, allowing the emergence of beneficial, but also detrimental, interactions among viruses inside infected cells. This has prompted interest among microbial ecologists and evolutionary biologists in studying how collective dispersal impacts the outcome of viral infections. Here, we have used vesicular stomatitis virus as a model system to study the evolutionary implications of collective dissemination mediated by viral aggregates, since this virus can spontaneously aggregate in the presence of saliva. We find that saliva-driven aggregation has a dual effect on viral fitness; whereas aggregation tends to increase infectivity in the very short term, virion aggregates are highly susceptible to invasion by noncooperative defective variants after a few viral generations.
Collapse
Affiliation(s)
- Iván Andreu-Moreno
- Institute for Integrative Systems Biology (ISysBio), Universitat de Valencia, Valencia, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (ISysBio), Universitat de Valencia, Valencia, Spain
| |
Collapse
|
36
|
[Structural studies on negative-strand RNA virus]. Uirusu 2020; 70:91-100. [PMID: 33967118 DOI: 10.2222/jsv.70.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Negative-strand RNA viruses do not possess a rigid viral shell, and their structures are flexible and fragile. We have applied various electron microscopies to analyze the morphologies of influenza and Ebola virus. Our studies have revealed the native interior and exterior ultrastructures of influenza virus as well as the assembly of Ebola virus core in atomic detail.
Collapse
|
37
|
Pavadai E, Bhattarai N, Baral P, Stahelin RV, Chapagain PP, Gerstman BS. Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. J Phys Chem B 2019; 123:9045-9053. [PMID: 31576755 DOI: 10.1021/acs.jpcb.9b04674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Ebola virus (EBOV) is a virulent pathogen that causes severe hemorrhagic fever with a high fatality rate in humans. The EBOV transformer protein VP40 plays crucial roles in viral assembly and budding at the plasma membrane of infected cells. One of VP40's roles is to form the long, flexible, pleomorphic filamentous structural matrix for the virus. Each filament contains three unique interfaces: monomer NTD-NTD to form a dimer, dimer-to-dimer NTD-NTD oligomerization to form a hexamer, and end-to-end hexamer CTD-CTD to build the filament. However, the atomic-level details of conformational flexibility of the VP40 filament are still elusive. In this study, we have performed explicit-solvent, all-atom molecular dynamic simulations to explore the conformational flexibility of the three different interface structures of the filament. Using dynamic network analysis and other calculational methods, we find that the CTD-CTD hexamer interface with weak interdomain amino acid communities is the most flexible, and the NTD-NTD oligomer interface with strong interdomain communities is the least flexible. Our study suggests that the high flexibility of the CTD-CTD interface may be essential for the supple bending of the Ebola filovirus, and such flexibility may present a target for molecular interventions to disrupt the Ebola virus functioning.
Collapse
Affiliation(s)
| | | | | | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue University Cancer Center , Purdue University , West Lafayette , Indiana 47907 , United States
| | | | | |
Collapse
|
38
|
Hume AJ, Mühlberger E. Distinct Genome Replication and Transcription Strategies within the Growing Filovirus Family. J Mol Biol 2019; 431:4290-4320. [PMID: 31260690 PMCID: PMC6879820 DOI: 10.1016/j.jmb.2019.06.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/31/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus genera and a sixth proposed genus. While two of these new genera are similar to the ebola- and marburgviruses, the other two, discovered in saltwater fishes, are considerably more diverse. Nonetheless, these viruses retain a number of key features of the other filoviruses. Here, we review the key characteristics of filovirus replication and transcription, highlighting similarities and differences between the viruses. In particular, we focus on key regulatory elements in the genomes, replication and transcription strategies, and the conservation of protein domains and functions among the viruses. In addition, using computational analyses, we were able to identify potential homology and functions for some of the genes of the novel filoviruses with previously unknown functions. Although none of the newly discovered filoviruses have yet been isolated, initial studies of some of these viruses using minigenome systems have yielded insights into their mechanisms of replication and transcription. In general, the Cuevavirus and proposed Dianlovirus genera appear to follow the transcription and replication strategies employed by the ebola- and marburgviruses, respectively. While our knowledge of the fish filoviruses is currently limited to sequence analysis, the lack of certain conserved motifs and even entire genes necessitates that they have evolved distinct mechanisms of replication and transcription.
Collapse
Affiliation(s)
- Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
| |
Collapse
|
39
|
Song X, Shan H, Zhu Y, Hu S, Xue L, Chen Y, Ding W, Niu T, Gu J, Ouyang S, Shen QT, Liu ZJ. Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome. eLife 2019; 8:45057. [PMID: 31290740 PMCID: PMC6675542 DOI: 10.7554/elife.45057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/09/2019] [Indexed: 12/02/2022] Open
Abstract
Non-segmented negative-strand RNA viruses, such as measles, ebola and Newcastle disease viruses (NDV), encapsidate viral genomic RNAs into helical nucleocapsids, which serve as the template for viral replication and transcription. Here, the clam-shaped nucleocapsid structure, where the NDV viral genome is sequestered, was determined at 4.8 Å resolution by cryo-electron microscopy. The clam-shaped structure is composed of two single-turn spirals packed in a back-to-back mode. This tightly packed structure functions as a seed for the assembly of a nucleocapsid from both directions, facilitating the growth of double-headed filaments with two separate RNA strings inside. Disruption of this structure by mutations in its loop interface yielded a single-headed unfunctional filament.
Collapse
Affiliation(s)
- Xiyong Song
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Shan
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Yanping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shunlin Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ling Xue
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Ding
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jian Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qing-Tao Shen
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Zhi-Jie Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,iHuman Institute, ShanghaiTech University, Shanghai, China
| |
Collapse
|
40
|
Ploquin A, Zhou Y, Sullivan NJ. Ebola Immunity: Gaining a Winning Position in Lightning Chess. THE JOURNAL OF IMMUNOLOGY 2019; 201:833-842. [PMID: 30038036 DOI: 10.4049/jimmunol.1700827] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 05/05/2018] [Indexed: 12/13/2022]
Abstract
Zaire ebolavirus (EBOV), one of five species in the genus Ebolavirus, is the causative agent of the hemorrhagic fever disease epidemic that claimed more than 11,000 lives from 2014 to 2016 in West Africa. The combination of EBOV's ability to disseminate broadly and rapidly within the host and its high pathogenicity pose unique challenges to the human immune system postinfection. Potential transmission from apparently healthy EBOV survivors reported in the recent epidemic raises questions about EBOV persistence and immune surveillance mechanisms. Clinical, virological, and immunological data collected since the West Africa epidemic have greatly enhanced our knowledge of host-virus interactions. However, critical knowledge gaps remain in our understanding of what is necessary for an effective host immune response for protection against, or for clearance of, EBOV infection. This review provides an overview of immune responses against EBOV and discusses those associated with the success or failure to control EBOV infection.
Collapse
Affiliation(s)
- Aurélie Ploquin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Yan Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
41
|
Abstract
This chapter reviews our current knowledge about the spatiotemporal assembly of filoviral particles. We will follow particles from nucleocapsid entry into the cytoplasm until the nucleocapsids are enveloped at the plasma membrane. We will also highlight the currently open scientific questions surrounding filovirus assembly.
Collapse
|
42
|
The effect of genetic complementation on the fitness and diversity of viruses spreading as collective infectious units. Virus Res 2019; 267:41-48. [PMID: 31077765 DOI: 10.1016/j.virusres.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/31/2022]
Abstract
Viruses can spread collectively using different types of structures such as extracellular vesicles, virion aggregates, polyploid capsids, occlusion bodies, and even cells that accumulate virions at their surface, such as bacteria and dendritic cells. Despite the mounting evidence for collective spread, its implications for viral fitness and diversity remain poorly understood. It has been postulated that, by increasing the cellular multiplicity of infection, collective spread could enable mutually beneficial interactions among different viral genetic variants. One such interaction is genetic complementation, whereby deleterious mutations carried by different genomes are compensated. Here, we used simulations to evaluate whether complementation is likely to increase the fitness of viruses spreading collectively. We show that complementation among co-spreading viruses initially buffers the deleterious effects of mutations, but has no positive effect on mean population fitness over the long term, and even promotes error catastrophe at high mutation rates. Additionally, we found that collective spread increases the risk of invasion by social cheaters such as defective interfering particles. We also show that mutation accumulation depends on the type of collective infectious units considered. Co-spreading viral genomes produced in the same cell (e.g. extracellular vesicles, polyploid capsids, occlusion bodies) should exhibit higher genetic relatedness than groups formed extracellularly by viruses released from different cells (aggregates, binding to bacterial or dendritic cell surfaces), and we found that increased relatedness limits the adverse effects of complementation as well cheater invasion risk. Finally, we found that the costs of complementation can be offset by recombination. Based on our results, we suggest that alternative factors promoting collective spread should be considered.
Collapse
|
43
|
Pleet ML, DeMarino C, Stonier SW, Dye JM, Jacobson S, Aman MJ, Kashanchi F. Extracellular Vesicles and Ebola Virus: A New Mechanism of Immune Evasion. Viruses 2019; 11:v11050410. [PMID: 31052499 PMCID: PMC6563240 DOI: 10.3390/v11050410] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
Ebola virus (EBOV) disease can result in a range of symptoms anywhere from virtually asymptomatic to severe hemorrhagic fever during acute infection. Additionally, spans of asymptomatic persistence in recovering survivors is possible, during which transmission of the virus may occur. In acute infection, substantial cytokine storm and bystander lymphocyte apoptosis take place, resulting in uncontrolled, systemic inflammation in affected individuals. Recently, studies have demonstrated the presence of EBOV proteins VP40, glycoprotein (GP), and nucleoprotein (NP) packaged into extracellular vesicles (EVs) during infection. EVs containing EBOV proteins have been shown to induce apoptosis in recipient immune cells, as well as contain pro-inflammatory cytokines. In this manuscript, we review the current field of knowledge on EBOV EVs including the mechanisms of their biogenesis, their cargo and their effects in recipient cells. Furthermore, we discuss some of the effects that may be induced by EBOV EVs that have not yet been characterized and highlight the remaining questions and future directions.
Collapse
Affiliation(s)
- Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Spencer W Stonier
- Department, Emergent BioSolutions, Gaithersburg, MD 20879, USA.
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - John M Dye
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Steven Jacobson
- Viral Immunology Section, Neuroimmunology Branch, National Institute for Neurological Disease and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - M Javad Aman
- Department. Integrated BioTherapeutics, Inc., Gaithersburg, MD 20850, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| |
Collapse
|
44
|
Kämper L, Zierke L, Schmidt ML, Müller A, Wendt L, Brandt J, Hartmann E, Braun S, Holzerland J, Groseth A, Hoenen T. Assessment of the function and intergenus-compatibility of Ebola and Lloviu virus proteins. J Gen Virol 2019; 100:760-772. [DOI: 10.1099/jgv.0.001261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Lennart Kämper
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Lukas Zierke
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Marie Luisa Schmidt
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Andreas Müller
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Lisa Wendt
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Janine Brandt
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Eric Hartmann
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Stefanie Braun
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Julia Holzerland
- 2 Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Allison Groseth
- 2 Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Thomas Hoenen
- 1 Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| |
Collapse
|
45
|
Antibody responses to viral infections: a structural perspective across three different enveloped viruses. Nat Microbiol 2019; 4:734-747. [PMID: 30886356 PMCID: PMC6818971 DOI: 10.1038/s41564-019-0392-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Antibodies serve as critical barriers to viral infection. Humoral immunity to a virus is achieved through the dual role of antibodies in communicating the presence of invading pathogens in infected cells to effector cells and interfering with processes essential to the viral lifecycle, chiefly entry into the host cell. For individuals that successfully control infection, virus-elicited antibodies can provide lifelong surveillance and protection from future insults. One approach to understand the nature of a successful immune response has been to utilize structural biology to uncover the molecular details of the antibodies derived from vaccines or natural infection and how they interact with their cognate microbial antigens. The ability to isolate antigen specific B-cells and rapidly solve structures of functional, monoclonal antibodies in complex with viral glycoprotein surface antigens has greatly expanded our knowledge of the sites of vulnerability on viruses. In this review, we compare the adaptive humoral immune responses to HIV, influenza, and filoviruses, with a particular focus on neutralizing antibodies. The pathogenesis of each of these viruses is quite different, providing an opportunity for comparison of immune responses: HIV causes a persistent, chronic infection; influenza an acute infection with multiple exposures during a lifetime and annual vaccination; and filoviruses, a virulent, acute infection. Neutralizing antibodies that develop under these different constraints are therefore sentinels that can provide insight into the underlying humoral immune responses and important lessons to guide future development of vaccines and immunotherapeutics.
Collapse
|
46
|
Shirogane Y, Watanabe S, Yanagi Y. Cooperation between different variants: A unique potential for virus evolution. Virus Res 2019; 264:68-73. [PMID: 30822430 DOI: 10.1016/j.virusres.2019.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 02/05/2023]
Abstract
RNA viruses exist as quasispecies containing many variants within their populations because of the error prone nature of viral RNA-dependent RNA polymerases. Quasispecies are not a simple collection of individual variants. Instead, internal interactions among variants provide quasispecies with unique evolvability. An example is 'cooperation' between wild-type and defective measles viruses, in which co-existence of a wild-type and a mutant genome produces a new phenotype. Such internal interactions presuppose efficient co-transmission of multiple genomes to the same cell, which is achieved by polyploid virions of some virus families or by a high multiplicity of infection. Recent studies have revealed that multiple viral genomes can also be transmitted simultaneously ('bloc transmission') by other mechanisms, strengthening the concept of internal interactions among viral quasispecies. Elucidation of the mechanisms of virus evolution, including internal interactions and bloc transmission, may provide rational strategies to solve such important problems of virus infections as drug-resistance, immune evasion, and acquisition of the new tropism and host range.
Collapse
Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
| | - Shumpei Watanabe
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-0085, Japan
| | - Yusuke Yanagi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
| |
Collapse
|
47
|
Brandt J, Wendt L, Hoenen T. Structure and functions of the Ebola virus matrix protein VP40. Future Virol 2019. [DOI: 10.2217/fvl-2018-0162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The matrix protein VP40 of the highly pathogenic Ebola virus (EBOV), a member of the filovirus family, is the most abundant protein in EBOV virions. During the viral life cycle it mediates assembly and budding from the host cell, and is responsible for the characteristic filamentous shape of EBOV particles. In addition to this classical function as a matrix protein, VP40 was also shown to have a regulatory function in viral transcription. To enable these distinct functions, VP40 can adopt different oligomeric states, in particular, dimers, hexamers and ring-like octameric RNA-binding structures. This review describes the properties and functions of the EBOV matrix protein VP40 and how these different conformations of VP40 contribute to its diverse functions.
Collapse
Affiliation(s)
- Janine Brandt
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald – Insel Riems, Germany
| | - Lisa Wendt
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald – Insel Riems, Germany
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald – Insel Riems, Germany
| |
Collapse
|
48
|
Pleet ML, Erickson J, DeMarino C, Barclay RA, Cowen M, Lepene B, Liang J, Kuhn JH, Prugar L, Stonier SW, Dye JM, Zhou W, Liotta LA, Aman MJ, Kashanchi F. Ebola Virus VP40 Modulates Cell Cycle and Biogenesis of Extracellular Vesicles. J Infect Dis 2018; 218:S365-S387. [PMID: 30169850 PMCID: PMC6249571 DOI: 10.1093/infdis/jiy472] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Ebola virus (EBOV) mainly targets myeloid cells; however, extensive death of T cells is often observed in lethal infections. We have previously shown that EBOV VP40 in exosomes causes recipient immune cell death. Methods Using VP40-producing clones, we analyzed donor cell cycle, extracellular vesicle (EV) biogenesis, and recipient immune cell death. Transcription of cyclin D1 and nuclear localization of VP40 were examined via kinase and chromatin immunoprecipitation assays. Extracellular vesicle contents were characterized by mass spectrometry, cytokine array, and western blot. Biosafety level-4 facilities were used for wild-type Ebola virus infection studies. Results VP40 EVs induced apoptosis in recipient T cells and monocytes. VP40 clones were accelerated in growth due to cyclin D1 upregulation, and nuclear VP40 was found bound to the cyclin D1 promoter. Accelerated cell cycling was related to EV biogenesis, resulting in fewer but larger EVs. VP40 EV contents were enriched in ribonucleic acid-binding proteins and cytokines (interleukin-15, transforming growth factor-β1, and interferon-γ). Finally, EBOV-infected cell and animal EVs contained VP40, nucleoprotein, and glycoprotein. Conclusions Nuclear VP40 upregulates cyclin D1 levels, resulting in dysregulated cell cycle and EV biogenesis. Packaging of cytokines and EBOV proteins into EVs from infected cells may be responsible for the decimation of immune cells during EBOV pathogenesis.
Collapse
Affiliation(s)
- Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| | - Robert A Barclay
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| | | | - Janie Liang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland
| | - Laura Prugar
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Spencer W Stonier
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - John M Dye
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - M Javad Aman
- Integrated BioTherapeutics, Inc., Gaithersburg, Maryland
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, Virginia
| |
Collapse
|
49
|
Sugita Y, Matsunami H, Kawaoka Y, Noda T, Wolf M. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution. Nature 2018; 563:137-140. [PMID: 30333622 DOI: 10.1038/s41586-018-0630-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA1,2. The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase1,3. The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion4,5. RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently6. Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core4,5, there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions that lead to the formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion5. The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.
Collapse
Affiliation(s)
- Yukihiko Sugita
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hideyuki Matsunami
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| |
Collapse
|
50
|
Sanjuán R. Collective properties of viral infectivity. Curr Opin Virol 2018; 33:1-6. [PMID: 30015082 DOI: 10.1016/j.coviro.2018.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
Individual virions typically fail to infect cells. Such decoupling between virions and infectious units is most evident in multicomponent and other segmented viruses, but is also frequent in non-segmented viruses. Despite being a well-known observation, the causes and implications of low single-virion infectivity often remain unclear. In principle, this can originate from intrinsic genetic and/or structural virion defects, but also from host infection barriers that limit early viral proliferation. Hence, viruses may have evolved strategies to increase the per-virion likelihood of establishing successful infections. This can be achieved by adopting spread modes that elevate the multiplicity of infection at the cellular level, including direct cell-to-cell viral transfer, encapsulation of multiple virions in microvesicles or other intercellular vehicles, virion aggregation, and virion binding to microbiota. In turn, increasing the multiplicity of infection could favor the evolution of defective viruses, hence modifying the fitness value of these spread modes.
Collapse
Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València 46980, Spain.
| |
Collapse
|