1
|
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
|
2
|
Narkhede Y, Saxena R, Sharma T, Conarty JP, Ramirez VT, Motsa BB, Amiar S, Li S, Chapagain PP, Wiest O, Stahelin RV. Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Sci 2024; 33:e4978. [PMID: 38591637 PMCID: PMC11002992 DOI: 10.1002/pro.4978] [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: 10/18/2023] [Revised: 02/01/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
The Ebola virus (EBOV) is a lipid-enveloped virus with a negative sense RNA genome that can cause severe and often fatal viral hemorrhagic fever. The assembly and budding of EBOV is regulated by the matrix protein, VP40, which is a peripheral protein that associates with anionic lipids at the inner leaflet of the plasma membrane. VP40 is sufficient to form virus-like particles (VLPs) from cells, which are nearly indistinguishable from authentic virions. Due to the restrictions of studying EBOV in BSL-4 facilities, VP40 has served as a surrogate in cellular studies to examine the EBOV assembly and budding process from the host cell plasma membrane. VP40 is a dimer where inhibition of dimer formation halts budding and formation of new VLPs as well as VP40 localization to the plasma membrane inner leaflet. To better understand VP40 dimer stability and critical amino acids to VP40 dimer formation, we integrated computational approaches with experimental validation. Site saturation/alanine scanning calculation, combined with molecular mechanics-based generalized Born with Poisson-Boltzmann surface area (MM-GB/PBSA) method and molecular dynamics simulations were used to predict the energetic contribution of amino acids to VP40 dimer stability and the hydrogen bonding network across the dimer interface. These studies revealed several previously unknown interactions and critical residues predicted to impact VP40 dimer formation. In vitro and cellular studies were then pursued for a subset of VP40 mutations demonstrating reduction in dimer formation (in vitro) or plasma membrane localization (in cells). Together, the computational and experimental approaches revealed critical residues for VP40 dimer stability in an alpha-helical interface (between residues 106-117) as well as in a loop region (between residues 52-61) below this alpha-helical region. This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability.
Collapse
Affiliation(s)
- Yogesh Narkhede
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Roopashi Saxena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Tej Sharma
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | - Jacob P. Conarty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Valentina Toro Ramirez
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
- Pharmaceutical ChemistryUniversidad CESMedellínColombia
| | - Balindile B. Motsa
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Souad Amiar
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| | - Sheng Li
- Department of MedicineUniversity of CaliforniaSan DiegoCaliforniaUSA
| | - Prem P. Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences Institute, Florida International UniversityMiamiFloridaUSA
| | - Olaf Wiest
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Robert V. Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and The Purdue Institute for Inflammation, Immunology and Infectious DiseasePurdue UniversityWest LafayetteIndianaUSA
| |
Collapse
|
3
|
Motsa BB, Sharma T, Cioffi MD, Chapagain PP, Stahelin RV. Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. J Biol Chem 2024; 300:107213. [PMID: 38522519 PMCID: PMC11061732 DOI: 10.1016/j.jbc.2024.107213] [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: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Ebola virus (EBOV) is a filamentous negative-sense RNA virus, which causes severe hemorrhagic fever. There are limited vaccines or therapeutics for prevention and treatment of EBOV, so it is important to get a detailed understanding of the virus lifecycle to illuminate new drug targets. EBOV encodes for the matrix protein, VP40, which regulates assembly and budding of new virions from the inner leaflet of the host cell plasma membrane (PM). In this work, we determine the effects of VP40 mutations altering electrostatics on PM interactions and subsequent budding. VP40 mutations that modify surface electrostatics affect viral assembly and budding by altering VP40 membrane-binding capabilities. Mutations that increase VP40 net positive charge by one (e.g., Gly to Arg or Asp to Ala) increase VP40 affinity for phosphatidylserine and phosphatidylinositol 4,5-bisphosphate in the host cell PM. This increased affinity enhances PM association and budding efficiency leading to more effective formation of virus-like particles. In contrast, mutations that decrease net positive charge by one (e.g., Gly to Asp) lead to a decrease in assembly and budding because of decreased interactions with the anionic PM. Taken together, our results highlight the sensitivity of slight electrostatic changes on the VP40 surface for assembly and budding. Understanding the effects of single amino acid substitutions on viral budding and assembly will be useful for explaining changes in the infectivity and virulence of different EBOV strains, VP40 variants that occur in nature, and for long-term drug discovery endeavors aimed at EBOV assembly and budding.
Collapse
Affiliation(s)
- Balindile B Motsa
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Tej Sharma
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Michael D Cioffi
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Robert V Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
| |
Collapse
|
4
|
Liu X, Husby M, Stahelin RV, Pienaar E. Evaluation of fendiline treatment in VP40 system with nucleation-elongation process: a computational model of Ebola virus matrix protein assembly. Microbiol Spectr 2024; 12:e0309823. [PMID: 38407984 PMCID: PMC10986538 DOI: 10.1128/spectrum.03098-23] [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: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Ebola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 laboratories hinder experimental work to advance our understanding of EBOV and the evaluation of treatment. In this work, we use a computational model to study the assembly and budding process of EBOV and evaluate the effect of fendiline on these processes in the context of fluctuating host membrane lipid levels. Our results demonstrate for the first time that the assembly of VP40 filaments may follow the nucleation-elongation theory, as this mechanism is critical to maintaining a pool of VP40 dimers for the maturation and production of virus-like particles (VLPs). We further find that this nucleation-elongation process is likely influenced by fluctuating phosphatidylserine (PS), which can complicate the efficacy of lipid-targeted therapies like fendiline, a drug that lowers cellular PS levels. Our results indicate that fendiline-induced PS reduction may actually increase VLP production at earlier time points (24 h) and under low fendiline concentrations (≤2 µM). However, this effect is transient and does not change the conclusion that fendiline generally decreases VLP production. In the context of fluctuating PS levels, we also conclude that fendiline can be more efficient at the late stage of VLP budding relative to earlier phases. Combination therapy with a VLP budding step-targeted drug may therefore further increase the treatment efficiency of fendiline. Finally, we also show that fendiline-induced PS reduction more effectively lowers VLP production when VP40 expression is high. Taken together, our results provide critical quantitative information on how fluctuating lipid levels (PS) affect EBOV assembly and egress and how this mechanism can be disrupted by lipid-targeting molecules like fendiline. IMPORTANCE Ebola virus (EBOV) infection can cause deadly hemorrhagic fever, which has a mortality rate of ~50%-90% without treatment. The recent outbreaks in Uganda and the Democratic Republic of the Congo illustrate its threat to human health. Though two antibody-based treatments were approved, mortality rates in the last outbreak were still higher than 30%. This can partly be due to the requirement of advanced medical facilities for current treatments. As a result, it is very important to develop and evaluate new therapies for EBOV infection, especially those that can be easily applied in the developing world. The significance of our research is that we evaluate the potential of lipid-targeted treatments in reducing EBOV assembly and egress. We achieved this goal using the VP40 system combined with a computational approach, which both saves time and lowers cost compared to traditional experimental studies and provides innovative new tools to study viral protein dynamics.
Collapse
Affiliation(s)
- Xiao Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Monica Husby
- 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
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
5
|
Cioffi MD, Husby ML, Gerstman BS, Stahelin RV, Chapagain PP. Role of phosphatidic acid lipids on plasma membrane association of the Ebola virus matrix protein VP40. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159464. [PMID: 38360201 DOI: 10.1016/j.bbalip.2024.159464] [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: 08/21/2023] [Revised: 01/14/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
The Ebola virus matrix protein VP40 is responsible for the formation of the viral matrix by localizing at the inner leaflet of the human plasma membrane (PM). Various lipid types, including PI(4,5)P2 (i.e. PIP2) and phosphatidylserine (PS), play active roles in this process. Specifically, the negatively charged headgroups of both PIP2 and PS interact with the basic residues of VP40 and stabilize it at the membrane surface, allowing for eventual egress. Phosphatidic acid (PA), resulting from the enzyme phospholipase D (PLD), is also known to play an active role in viral development. In this work, we performed a biophysical and computational analysis to investigate the effects of the presence of PA on the membrane localization and association of VP40. We used coarse-grained molecular dynamics simulations to quantify VP40 hexamer interactions with the inner leaflet of the PM. Analysis of the local distribution of lipids shows enhanced lipid clustering when PA is abundant in the membrane. We observed that PA lipids have a similar role to that of PS lipids in VP40 association due to the geometry and charge. Complementary experiments performed in cell culture demonstrate competition between VP40 and a canonical PA-binding protein for the PM. Also, inhibition of PA synthesis reduced the detectable budding of virus-like particles. These computational and experimental results provide new insights into the early stages of Ebola virus budding and the role that PA lipids have on the VP40-PM association.
Collapse
Affiliation(s)
- Michael D Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Monica L Husby
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; The Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
| |
Collapse
|
6
|
Johnson KA, Budicini MR, Bhattarai N, Sharma T, Urata S, Gerstman BS, Chapagain PP, Li S, Stahelin RV. PI(4,5)P 2 binding sites in the Ebola virus matrix protein VP40 modulate assembly and budding. J Lipid Res 2024; 65:100512. [PMID: 38295986 PMCID: PMC10909612 DOI: 10.1016/j.jlr.2024.100512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
Ebola virus (EBOV) causes severe hemorrhagic fever in humans and is lethal in a large percentage of those infected. The EBOV matrix protein viral protein 40 kDa (VP40) is a peripheral binding protein that forms a shell beneath the lipid bilayer in virions and virus-like particles (VLPs). VP40 is required for virus assembly and budding from the host cell plasma membrane. VP40 is a dimer that can rearrange into oligomers at the plasma membrane interface, but it is unclear how these structures form and how they are stabilized. We therefore investigated the ability of VP40 to form stable oligomers using in vitro and cellular assays. We characterized two lysine-rich regions in the VP40 C-terminal domain (CTD) that bind phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and play distinct roles in lipid binding and the assembly of the EBOV matrix layer. The extensive analysis of VP40 with and without lipids by hydrogen deuterium exchange mass spectrometry revealed that VP40 oligomers become extremely stable when VP40 binds PI(4,5)P2. The PI(4,5)P2-induced stability of VP40 dimers and oligomers is a critical factor in VP40 oligomerization and release of VLPs from the plasma membrane. The two lysine-rich regions of the VP40 CTD have different roles with respect to interactions with plasma membrane phosphatidylserine (PS) and PI(4,5)P2. CTD region 1 (Lys221, Lys224, and Lys225) interacts with PI(4,5)P2 more favorably than PS and is important for VP40 extent of oligomerization. In contrast, region 2 (Lys270, Lys274, Lys275, and Lys279) mediates VP40 oligomer stability via lipid interactions and has a more prominent role in release of VLPs.
Collapse
Affiliation(s)
- Kristen A Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Melissa R Budicini
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL, USA
| | - Tej Sharma
- Department of Physics, Florida International University, Miami, FL, USA
| | - Sarah Urata
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Sheng Li
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
7
|
Motsa BB, Sharma T, Chapagain PP, Stahelin RV. Minor changes in electrostatics robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578092. [PMID: 38352396 PMCID: PMC10862912 DOI: 10.1101/2024.01.30.578092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ebola virus (EBOV) is a filamentous negative-sense RNA virus which causes severe hemorrhagic fever. There are limited vaccines or therapeutics for prevention and treatment of EBOV, so it is important to get a detailed understanding of the virus lifecycle to illuminate new drug targets. EBOV encodes for the matrix protein, VP40, which regulates assembly and budding of new virions from the inner leaflet of the host cell plasma membrane (PM). In this work we determine the effects of VP40 mutations altering electrostatics on PM interactions and subsequent budding. VP40 mutations that modify surface electrostatics affect viral assembly and budding by altering VP40 membrane binding capabilities. Mutations that increase VP40 net positive charge by one (e.g., Gly to Arg or Asp to Ala) increase VP40 affinity for phosphatidylserine (PS) and PI(4,5)P2 in the host cell PM. This increased affinity enhances PM association and budding efficiency leading to more effective formation of virus-like particles (VLPs). In contrast, mutations that decrease net positive charge by one (e.g., Gly to Asp) lead to a decrease in assembly and budding because of decreased interactions with the anionic PM. Taken together our results highlight the sensitivity of slight electrostatic changes on the VP40 surface for assembly and budding. Understanding the effects of single amino acid substitutions on viral budding and assembly will be useful for explaining changes in the infectivity and virulence of different EBOV strains, VP40 variants that occur in nature, and for long-term drug discovery endeavors aimed at EBOV assembly and budding.
Collapse
Affiliation(s)
- Balindile B. Motsa
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V. Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
8
|
Saphire E, Salie ZL, Ke Z, Halfmann P, DeWald LE, McArdle S, Grinyo A, Davidson E, Schendel S, Hariharan C, Norris M, Yu X, Chennareddy C, Xiong X, Heinrich M, Holbrook M, Doranz B, Crozier I, Hastie K, Kawaoka Y, Branco L, Kuhn J, Briggs J, Worwa G, Davis C, Ahmed R. Anti-Ebola virus mAb 3A6 with unprecedented potency protects highly viremic animals from fatal outcome and physically lifts its glycoprotein target from the virion membrane. RESEARCH SQUARE 2023:rs.3.rs-3722563. [PMID: 38196595 PMCID: PMC10775387 DOI: 10.21203/rs.3.rs-3722563/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP1,2) are the standard of care for Ebola virus disease (EVD). Anti-GP1,2 mAbs targeting the stalk and membrane proximal external region (MPER) potently neutralize EBOV in vitro. However, their neutralization mechanism is poorly understood because they target a GP1,2 epitope that has evaded structural characterization. Moreover, their in vivo efficacy has only been evaluated in the mouse model of EVD. Using x-ray crystallography and cryo-electron tomography of 3A6 complexed with its stalk- GP1,2 MPER epitope we reveal a novel mechanism in which 3A6 elevates the stalk or stabilizes a conformation of GP1,2 that is lifted from the virion membrane. In domestic guinea pig and rhesus monkey EVD models, 3A6 provides therapeutic benefit at high viremia levels, advanced disease stages, and at the lowest dose yet demonstrated for any anti-EBOV mAb-based monotherapy. These findings can guide design of next-generation, highly potent anti-EBOV mAbs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xiaoli Xiong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
| | | | - Michael Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Bodmer BS, Breithaupt A, Heung M, Brunetti JE, Henkel C, Müller-Guhl J, Rodríguez E, Wendt L, Winter SL, Vallbracht M, Müller A, Römer S, Chlanda P, Muñoz-Fontela C, Hoenen T, Escudero-Pérez B. In vivo characterization of the novel ebolavirus Bombali virus suggests a low pathogenic potential for humans. Emerg Microbes Infect 2023; 12:2164216. [PMID: 36580440 PMCID: PMC9858441 DOI: 10.1080/22221751.2022.2164216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ebolaviruses cause outbreaks of haemorrhagic fever in Central and West Africa. Some members of this genus such as Ebola virus (EBOV) are highly pathogenic, with case fatality rates of up to 90%, whereas others such as Reston virus (RESTV) are apathogenic for humans. Bombali virus (BOMV) is a novel ebolavirus for which complete genome sequences were recently found in free-tailed bats, although no infectious virus could be isolated. Its pathogenic potential for humans is unknown. To address this question, we first determined whether proteins encoded by the available BOMV sequence found in Chaerephon pumilus were functional in in vitro assays. The correction of an apparent sequencing error in the glycoprotein based on these data then allowed us to generate infectious BOMV using reverse genetics and characterize its infection of human cells. Furthermore, we used HLA-A2-transgenic, NOD-scid-IL-2γ receptor-knockout (NSG-A2) mice reconstituted with human haematopoiesis as a model to evaluate the pathogenicity of BOMV in vivo in a human-like immune environment. These data demonstrate that not only does BOMV show a slower growth rate than EBOV in vitro, but it also shows low pathogenicity in humanized mice, comparable to previous studies using RESTV. Taken together, these findings suggest a low pathogenic potential of BOMV for humans.
Collapse
Affiliation(s)
- B. S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - A. Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - M. Heung
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J. E. Brunetti
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - C. Henkel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J. Müller-Guhl
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Leibniz Institute of Virology, Hamburg, Germany
| | - E. Rodríguez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Braunschweig, Germany
| | - L. Wendt
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - S. L. Winter
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - M. Vallbracht
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - A. Müller
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - S. Römer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - P. Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - C. Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Braunschweig, Germany
| | - T. Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany, T. Hoenen Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald – Insel Riems, 17493Germany
| | - B. Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Braunschweig, Germany
| |
Collapse
|
10
|
Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [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: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
Collapse
Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
11
|
Werner AD, Schauflinger M, Norris MJ, Klüver M, Trodler A, Herwig A, Brandstädter C, Dillenberger M, Klebe G, Heine A, Saphire EO, Becker K, Becker S. The C-terminus of Sudan ebolavirus VP40 contains a functionally important CX nC motif, a target for redox modifications. Structure 2023; 31:1038-1051.e7. [PMID: 37392738 DOI: 10.1016/j.str.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/10/2023] [Accepted: 06/06/2023] [Indexed: 07/03/2023]
Abstract
The Ebola virus matrix protein VP40 mediates viral budding and negatively regulates viral RNA synthesis. The mechanisms by which these two functions are exerted and regulated are unknown. Using a high-resolution crystal structure of Sudan ebolavirus (SUDV) VP40, we show here that two cysteines in the flexible C-terminal arm of VP40 form a stabilizing disulfide bridge. Notably, the two cysteines are targets of posttranslational redox modifications and interact directly with the host`s thioredoxin system. Mutation of the cysteines impaired the budding function of VP40 and relaxed its inhibitory role for viral RNA synthesis. In line with these results, the growth of recombinant Ebola viruses carrying cysteine mutations was impaired and the released viral particles were elongated. Our results revealed the exact positions of the cysteines in the C-terminal arm of SUDV VP40. The cysteines and/or their redox status are critically involved in the differential regulation of viral budding and viral RNA synthesis.
Collapse
Affiliation(s)
| | | | - Michael J Norris
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Michael Klüver
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Anna Trodler
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Astrid Herwig
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Christina Brandstädter
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | | | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Stephan Becker
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany.
| |
Collapse
|
12
|
Zinzula L. Ebolavirus VP40 redux. Or rather, redox. Structure 2023; 31:1008-1010. [PMID: 37683615 DOI: 10.1016/j.str.2023.08.010] [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: 08/05/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
The virion protein 40 (VP40) forms the viral matrix, mediates budding, and downregulates viral RNA synthesis in ebolaviruses. In this issue of Structure, Werner et al. present a structure of VP40 from Sudan ebolavirus with a previously unresolved disulfide bridge that enables regulation of VP40 functions via human thioredoxin.
Collapse
Affiliation(s)
- Luca Zinzula
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
13
|
Lata K, Charles S, Mangala Prasad V. Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy. J Struct Biol 2023; 215:107993. [PMID: 37414374 DOI: 10.1016/j.jsb.2023.107993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.
Collapse
Affiliation(s)
- Kiran Lata
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sylvia Charles
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Vidya Mangala Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India; Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| |
Collapse
|
14
|
Liu X, Husby M, Stahelin RV, Pienaar E. Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551833. [PMID: 37577722 PMCID: PMC10418208 DOI: 10.1101/2023.08.03.551833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Ebola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 (BSL-4) laboratories hinders experimental work to advance our understanding of EBOV and evaluation of treatment. In this work, we use a computational model to study the assembly and budding process of EBOV and evaluate the effect of fendiline on these processes. Our results indicate that the assembly of VP40 filaments may follow the nucleation-elongation theory, as it is critical to maintain a pool of VP40 dimer for the maturation and production of virus-like particles (VLPs). We further find that the nucleation-elongation process can also be influenced by phosphatidylserine (PS), which can complicate the efficacy of fendiline, a drug that lowers cellular PS levels. We observe that fendiline may increase VLP production at earlier time points (24 h) and under low concentrations (≤ 2 μM). But this effect is transient and does not change the conclusion that fendiline generally decreases VLP production. We also conclude that fendiline can be more efficient at the stage of VLP budding relative to earlier phases. Combination therapy with a VLP budding step-targeted drug may further increase the treatment efficiency of fendiline. Finally, we also show that fendiline has higher efficacy when VP40 expression is high. While these are single-cell level results based on the VP40 system, it points out a potential way of fendiline application affecting EBOV assembly, which can be further tested in experimental studies with multiple EBOV proteins or live virus.
Collapse
Affiliation(s)
- Xiao Liu
- Weldon School of Biomedical Engineering, Purdue University
| | - Monica Husby
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University
- Regenstrief Center for Healthcare Engineering, Purdue University
| |
Collapse
|
15
|
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
|
16
|
Zimmermann L, Chlanda P. Cryo-electron tomography of viral infection - from applications to biosafety. Curr Opin Virol 2023; 61:101338. [PMID: 37348443 DOI: 10.1016/j.coviro.2023.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/25/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Cellular cryo-electron tomography (cryo-ET) offers 3D snapshots at molecular resolution capturing pivotal steps during viral infection. However, tomogram quality depends on the vitrification level of the sample and its thickness. In addition, mandatory inactivation protocols to assure biosafety when handling highly pathogenic viruses during cryo-ET can compromise sample preservation. Here, we focus on different strategies applied in cryo-ET and discuss their advantages and limitations with reference to severe acute respiratory syndrome coronavirus 2 studies. We highlight the importance of virus-like particle (VLP) and replicon systems to study virus assembly and replication in a cellular context without inactivation protocols. We discuss the application of chemical fixation and different irradiation methods in cryo-ET sample preparation and acquisition workflows.
Collapse
Affiliation(s)
- Liv Zimmermann
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| |
Collapse
|
17
|
Winter SL, Golani G, Lolicato F, Vallbracht M, Thiyagarajah K, Ahmed SS, Lüchtenborg C, Fackler OT, Brügger B, Hoenen T, Nickel W, Schwarz US, Chlanda P. The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion. EMBO J 2023:e113578. [PMID: 37082863 DOI: 10.15252/embj.2023113578] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Ebola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating, including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.
Collapse
Affiliation(s)
- Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Gonen Golani
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Melina Vallbracht
- Schaller Research Groups, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Keerthihan Thiyagarajah
- Schaller Research Groups, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Samy Sid Ahmed
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Insitut, Greifswald-Insel Riems, Greifswald, Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Ulrich S Schwarz
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
18
|
Dutka P, Metskas LA, Hurt RC, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TF, Shapiro MG, Jensen GJ. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 2023; 31:518-528.e6. [PMID: 37040766 PMCID: PMC10185304 DOI: 10.1016/j.str.2023.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
Collapse
Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hossein Salahshoor
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
| |
Collapse
|
19
|
Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
Collapse
Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
| |
Collapse
|
20
|
Hyun J. Poxvirus under the eyes of electron microscope. Appl Microsc 2022; 52:11. [DOI: 10.1186/s42649-022-00080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractZoonotic poxvirus infections pose significant threat to human health as we have witnessed recent spread of monkeypox. Therefore, insights into molecular mechanism behind poxvirus replication cycle are needed for the development of efficient antiviral strategies. Virion assembly is one of the key steps that determine the fate of replicating poxviruses. However, in-depth understanding of poxvirus assembly is challenging due to the complex nature of multi-step morphogenesis and heterogeneous virion structures. Despite these challenges, decades of research have revealed virion morphologies at various maturation stages, critical protein components and interactions with host cell compartments. Transmission electron microscopy has been employed as an indispensable tool for the examination of virion morphology, and more recently for the structure determination of protein complexes. In this review, we describe some of the major findings in poxvirus morphogenesis and the contributions of continuously advancing electron microscopy techniques.
Collapse
|
21
|
Husby ML, Amiar S, Prugar LI, David EA, Plescia CB, Huie KE, Brannan JM, Dye JM, Pienaar E, Stahelin RV. Phosphatidylserine clustering by the Ebola virus matrix protein is a critical step in viral budding. EMBO Rep 2022; 23:e51709. [PMID: 36094794 PMCID: PMC9638875 DOI: 10.15252/embr.202051709] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 07/28/2023] Open
Abstract
Phosphatidylserine (PS) is a critical lipid factor in the assembly and spread of numerous lipid-enveloped viruses. Here, we describe the ability of the Ebola virus (EBOV) matrix protein eVP40 to induce clustering of PS and promote viral budding in vitro, as well as the ability of an FDA-approved drug, fendiline, to reduce PS clustering and subsequent virus budding and entry. To gain mechanistic insight into fendiline inhibition of EBOV replication, multiple in vitro assays were run including imaging, viral budding and viral entry assays. Fendiline lowers PS content in mammalian cells and PS in the plasma membrane, where the ability of VP40 to form new virus particles is greatly lower. Further, particles that form from fendiline-treated cells have altered particle morphology and cannot significantly infect/enter cells. These complementary studies reveal the mechanism by which EBOV matrix protein clusters PS to enhance viral assembly, budding, and spread from the host cell while also laying the groundwork for fundamental drug targeting strategies.
Collapse
Affiliation(s)
- Monica L Husby
- Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteINUSA
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D)Purdue University, West LafayetteWest LafayetteINUSA
| | - Souad Amiar
- Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteINUSA
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D)Purdue University, West LafayetteWest LafayetteINUSA
| | - Laura I Prugar
- United States Army Medical Research Institute of Infectious Diseases USAMRIIDFort DetrickFrederickMDUSA
| | - Emily A David
- Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteINUSA
| | - Caroline B Plescia
- Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteINUSA
| | - Kathleen E Huie
- United States Army Medical Research Institute of Infectious Diseases USAMRIIDFort DetrickFrederickMDUSA
| | - Jennifer M Brannan
- United States Army Medical Research Institute of Infectious Diseases USAMRIIDFort DetrickFrederickMDUSA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases USAMRIIDFort DetrickFrederickMDUSA
| | - Elsje Pienaar
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D)Purdue University, West LafayetteWest LafayetteINUSA
- Weldon School of Biomedical EngineeringPurdue UniversityWest LafayetteINUSA
| | - Robert V Stahelin
- Department of Medicinal Chemistry & Molecular PharmacologyPurdue UniversityWest LafayetteINUSA
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D)Purdue University, West LafayetteWest LafayetteINUSA
| |
Collapse
|
22
|
Zhou K, Si Z, Ge P, Tsao J, Luo M, Zhou ZH. Atomic model of vesicular stomatitis virus and mechanism of assembly. Nat Commun 2022; 13:5980. [PMID: 36216930 PMCID: PMC9549855 DOI: 10.1038/s41467-022-33664-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
Like other negative-strand RNA viruses (NSVs) such as influenza and rabies, vesicular stomatitis virus (VSV) has a three-layered organization: a layer of matrix protein (M) resides between the glycoprotein (G)-studded membrane envelope and the nucleocapsid, which is composed of the nucleocapsid protein (N) and the encapsidated genomic RNA. Lack of in situ atomic structures of these viral components has limited mechanistic understanding of assembling the bullet-shaped virion. Here, by cryoEM and sub-particle reconstruction, we have determined the in situ structures of M and N inside VSV at 3.47 Å resolution. In the virion, N and M sites have a stoichiometry of 1:2. The in situ structures of both N and M differ from their crystal structures in their N-terminal segments and oligomerization loops. N-RNA, N-N, and N-M-M interactions govern the formation of the capsid. A double layer of M contributes to packaging of the helical nucleocapsid: the inner M (IM) joins neighboring turns of the N helix, while the outer M (OM) contacts G and the membrane envelope. The pseudo-crystalline organization of G is further mapped by cryoET. The mechanism of VSV assembly is delineated by the network interactions of these viral components. Zhou and Si et al. used cryogenic electron microscopy and tomography to delineate the molecular interactions among genomic RNA, nucleocapsid protein, matrix protein and glycoprotein in vesicular stomatitis virus and suggest a model of assembly.
Collapse
Affiliation(s)
- Kang Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhu Si
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Peng Ge
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.,Departments of Chemistry and Biochemistry and Biological Chemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Jun Tsao
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Al, 35294, USA
| | - Ming Luo
- The Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA. .,California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
| |
Collapse
|
23
|
Norris MJ, Husby ML, Kiosses WB, Yin J, Saxena R, Rennick LJ, Heiner A, Harkins SS, Pokhrel R, Schendel SL, Hastie KM, Landeras-Bueno S, Salie ZL, Lee B, Chapagain PP, Maisner A, Duprex WP, Stahelin RV, Saphire EO. Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. SCIENCE ADVANCES 2022; 8:eabn1440. [PMID: 35857835 PMCID: PMC9299542 DOI: 10.1126/sciadv.abn1440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/06/2022] [Indexed: 05/03/2023]
Abstract
Measles virus, Nipah virus, and multiple other paramyxoviruses cause disease outbreaks in humans and animals worldwide. The paramyxovirus matrix (M) protein mediates virion assembly and budding from host cell membranes. M is thus a key target for antivirals, but few high-resolution structures of paramyxovirus M are available, and we lack the clear understanding of how viral M proteins interact with membrane lipids to mediate viral assembly and egress that is needed to guide antiviral design. Here, we reveal that M proteins associate with phosphatidylserine and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the plasma membrane. Using x-ray crystallography, electron microscopy, and molecular dynamics, we demonstrate that PI(4,5)P2 binding induces conformational and electrostatic changes in the M protein surface that trigger membrane deformation, matrix layer polymerization, and virion assembly.
Collapse
Affiliation(s)
- Michael J. Norris
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Monica L. Husby
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - William B. Kiosses
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Jieyun Yin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Roopashi Saxena
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Linda J. Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Anja Heiner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Stephanie S. Harkins
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Sharon L. Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Zhe Li Salie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - W. Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| |
Collapse
|
24
|
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
|
25
|
Protein Folding Interdiction Strategy for Therapeutic Drug Development in Viral Diseases: Ebola VP40 and Influenza A M1. Int J Mol Sci 2022; 23:ijms23073906. [PMID: 35409264 PMCID: PMC8998936 DOI: 10.3390/ijms23073906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
In a recent paper, we proposed the folding interdiction target region (FITR) strategy for therapeutic drug design in SARS-CoV-2. This paper expands the application of the FITR strategy by proposing therapeutic drug design approaches against Ebola virus disease and influenza A. We predict target regions for folding interdicting drugs on correspondingly relevant structural proteins of both pathogenic viruses: VP40 of Ebola, and matrix protein M1 of influenza A. Identification of the protein targets employs the sequential collapse model (SCM) for protein folding. It is explained that the model predicts natural peptide candidates in each case from which to start the search for therapeutic drugs. The paper also discusses how these predictions could be tested, as well as some challenges likely to be found when designing effective therapeutic drugs from the proposed peptide candidates. The FITR strategy opens a potential new avenue for the design of therapeutic drugs that promises to be effective against infectious diseases.
Collapse
|
26
|
Vankadari N, Shepherd DC, Carter SD, Ghosal D. Three-dimensional insights into human enveloped viruses in vitro and in situ. Biochem Soc Trans 2022; 50:95-105. [PMID: 35076655 PMCID: PMC9022983 DOI: 10.1042/bst20210433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022]
Abstract
Viruses can be enveloped or non-enveloped, and require a host cell to replicate and package their genomes into new virions to infect new cells. To accomplish this task, viruses hijack the host-cell machinery to facilitate their replication by subverting and manipulating normal host cell function. Enveloped viruses can have severe consequences for human health, causing various diseases such as acquired immunodeficiency syndrome (AIDS), seasonal influenza, COVID-19, and Ebola virus disease. The complex arrangement and pleomorphic architecture of many enveloped viruses pose a challenge for the more widely used structural biology techniques, such as X-ray crystallography. Cryo-electron tomography (cryo-ET), however, is a particularly well-suited tool for overcoming the limitations associated with visualizing the irregular shapes and morphology enveloped viruses possess at macromolecular resolution. The purpose of this review is to explore the latest structural insights that cryo-ET has revealed about enveloped viruses, with particular attention given to their architectures, mechanisms of entry, replication, assembly, maturation and egress during infection. Cryo-ET is unique in its ability to visualize cellular landscapes at 3-5 nanometer resolution. Therefore, it is the most suited technique to study asymmetric elements and structural rearrangements of enveloped viruses during infection in their native cellular context.
Collapse
Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Doulin C. Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen D. Carter
- Centre for Virus Research, Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, U.K
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
27
|
Bhattarai N, Pavadai E, Pokhrel R, Baral P, Hossen L, Stahelin RV, Chapagain PP, Gerstman BS. Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane. Proteins 2022; 90:340-350. [PMID: 34431571 PMCID: PMC8738135 DOI: 10.1002/prot.26221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023]
Abstract
Outbreaks of the Ebola virus (EBOV) continue to occur and while a vaccine and treatment are now available, there remains a dearth of options for those who become sick with EBOV disease. An understanding at the atomic and molecular level of the various steps in the EBOV replication cycle can provide molecular targets for disrupting the virus. An important step in the EBOV replication cycle is the transport of EBOV structural matrix VP40 protein molecules to the plasma membrane inner leaflet, which involves VP40 binding to the host cell's Sec24c protein. Though some VP40 residues involved in the binding are known, the molecular details of VP40-Sec24c binding are not known. We use various molecular computational techniques to investigate the molecular details of how EBOV VP40 binds with the Sec24c complex of the ESCRT-I pathway. We employed different docking programs to identify the VP40-binding site on Sec24c and then performed molecular dynamics simulations to determine the atomic details and binding interactions of the complex. We also investigated how the inter-protein interactions of the complex are affected upon mutations of VP40 amino acids in the Sec24c-binding region. Our results provide a molecular basis for understanding previous coimmunoprecipitation experimental studies. In addition, we found that VP40 can bind to a site on Sec24c that can also bind Sec23 and suggests that VP40 may use the COPII transport mechanism in a manner that may not need the Sec23 protein in order for VP40 to be transported to the plasma membrane.
Collapse
Affiliation(s)
- Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Elumalai Pavadai
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Lokman Hossen
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette IN 47906
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
28
|
Husby ML, Stahelin RV. Negative-sense RNA viruses: An underexplored platform for examining virus-host lipid interactions. Mol Biol Cell 2021; 32:pe1. [PMID: 34570653 PMCID: PMC8684762 DOI: 10.1091/mbc.e19-09-0490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 11/11/2022] Open
Abstract
Viruses are pathogenic agents that can infect all varieties of organisms, including plants, animals, and humans. These microscopic particles are genetically simple as they encode a limited number of proteins that undertake a wide range of functions. While structurally distinct, viruses often share common characteristics that have evolved to aid in their infectious life cycles. A commonly underappreciated characteristic of many deadly viruses is a lipid envelope that surrounds their protein and genetic contents. Notably, the lipid envelope is formed from the host cell the virus infects. Lipid-enveloped viruses comprise a diverse range of pathogenic viruses, which often lead to high fatality rates and many lack effective therapeutics and/or vaccines. This perspective primarily focuses on the negative-sense RNA viruses from the order Mononegavirales, which obtain their lipid envelope from the host plasma membrane. Specifically, the perspective highlights the common themes of host cell lipid and membrane biology necessary for virus replication, assembly, and budding.
Collapse
Affiliation(s)
- Monica L. Husby
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907
| |
Collapse
|
29
|
Li S. Cryo-electron tomography of enveloped viruses. Trends Biochem Sci 2021; 47:173-186. [PMID: 34511334 DOI: 10.1016/j.tibs.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Viruses are macromolecular machineries that hijack cellular metabolism for replication. Enveloped viruses comprise a large variety of RNA and DNA viruses, many of which are notorious human or animal pathogens. Despite their importance, the presence of lipid bilayers in their assembly has made most enveloped viruses too pleomorphic to be reconstructed as a whole by traditional structural biology methods. Furthermore, structural biology of the viral lifecycle was hindered by the sample thickness. Here, I review the recent advances in the applications of cryo-electron tomography (cryo-ET) on enveloped viral structures and intracellular viral activities.
Collapse
Affiliation(s)
- Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
30
|
Lipid-protein interactions in virus assembly and budding from the host cell plasma membrane. Biochem Soc Trans 2021; 49:1633-1641. [PMID: 34431495 PMCID: PMC8421045 DOI: 10.1042/bst20200854] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 12/25/2022]
Abstract
Lipid enveloped viruses contain a lipid bilayer coat that protects their genome to help facilitate entry into the new host cell. This lipid bilayer comes from the host cell which they infect. After viral replication, the mature virion hijacks the host cell plasma membrane where it is then released to infect new cells. This process is facilitated by the interaction between phospholipids that make up the plasma membrane and specialized viral matrix proteins. This step in the viral lifecycle may represent a viable therapeutic strategy for small molecules that aim to block enveloped virus spread. In this review, we summarize the current knowledge on the role of plasma membrane lipid-protein interactions on viral assembly and budding.
Collapse
|
31
|
Johnson KA, Bhattarai N, Budicini MR, LaBonia CM, Baker SCB, Gerstman BS, Chapagain PP, Stahelin RV. Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop. Viruses 2021; 13:1375. [PMID: 34372582 PMCID: PMC8310056 DOI: 10.3390/v13071375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022] Open
Abstract
Ebolavirus (EBOV) is a negative-sense RNA virus that causes severe hemorrhagic fever in humans. The matrix protein VP40 facilitates viral budding by binding to lipids in the host cell plasma membrane and driving the formation of filamentous, pleomorphic virus particles. The C-terminal domain of VP40 contains two highly-conserved cysteine residues at positions 311 and 314, but their role in the viral life cycle is unknown. We therefore investigated the properties of VP40 mutants in which the conserved cysteine residues were replaced with alanine. The C311A mutation significantly increased the affinity of VP40 for membranes containing phosphatidylserine (PS), resulting in the assembly of longer virus-like particles (VLPs) compared to wild-type VP40. The C314A mutation also increased the affinity of VP40 for membranes containing PS, albeit to a lesser degree than C311A. The double mutant behaved in a similar manner to the individual mutants. Computer modeling revealed that both cysteine residues restrain a loop segment containing lysine residues that interact with the plasma membrane, but Cys311 has the dominant role. Accordingly, the C311A mutation increases the flexibility of this membrane-binding loop, changes the profile of hydrogen bonding within VP40 and therefore binds to PS with greater affinity. This is the first evidence that mutations in VP40 can increase its affinity for biological membranes and modify the length of Ebola VLPs. The Cys311 and Cys314 residues therefore play an important role in dynamic interactions at the plasma membrane by modulating the ability of VP40 to bind PS.
Collapse
Affiliation(s)
- Kristen A. Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
| | - Melissa R. Budicini
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Carolyn M. LaBonia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Sarah Catherine B. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
- The Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
- The Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
32
|
P300-mediated NEDD4 acetylation drives ebolavirus VP40 egress by enhancing NEDD4 ligase activity. PLoS Pathog 2021; 17:e1009616. [PMID: 34111220 PMCID: PMC8191996 DOI: 10.1371/journal.ppat.1009616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
The final stage of Ebola virus (EBOV) replication is budding from host cells, where the matrix protein VP40 is essential for driving this process. Many post-translational modifications such as ubiquitination are involved in VP40 egress, but acetylation has not been studied yet. Here, we characterize NEDD4 is acetylated at a conserved Lys667 mediated by the acetyltransferase P300 which drives VP40 egress process. Importantly, P300-mediated NEDD4 acetylation promotes NEDD4-VP40 interaction which enhances NEDD4 E3 ligase activity and is essential for the activation of VP40 ubiquitination and subsequent egress. Finally, we find that Zaire ebolavirus production is dramatically reduced in P300 knockout cell lines, suggesting that P300-mediated NEDD4 acetylation may have a physiological effect on Ebola virus life cycle. Thus, our study identifies an acetylation-dependent regulatory mechanism that governs VP40 ubiquitination and provides insights into how acetylation controls EBOV VP40 egress. Ebola virus (EBOV) is one of the deadliest pathogens, causing fatal hemorrhagic fever diseases in humans and primates. In this study, we find that P300-mediated NEDD4 acetylation facilitates EBOV egress. Acetylation promotes NEDD4-VP40 interactions which enhances NEDD4 E3 ligase activity and is essential for the activation of VP40 ubiquitination and subsequent egress. This study implies that inhibitory effect of acetylation can be regarded as an attractive candidate of drug target for the treatment of Ebola virus disease.
Collapse
|
33
|
Amiar S, Husby ML, Wijesinghe KJ, Angel S, Bhattarai N, Gerstman BS, Chapagain PP, Li S, Stahelin RV. Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. J Biol Chem 2021; 296:100796. [PMID: 34019871 PMCID: PMC8191294 DOI: 10.1016/j.jbc.2021.100796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 02/03/2023] Open
Abstract
Marburg virus (MARV) is a lipid-enveloped virus harboring a negative-sense RNA genome, which has caused sporadic outbreaks of viral hemorrhagic fever in sub-Saharan Africa. MARV assembles and buds from the host cell plasma membrane where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. The MARV matrix layer confers the virion filamentous shape and stability but how host lipids modulate mVP40 oligomerization is mostly unknown. Using in vitro and cellular techniques, we present a mVP40 assembly model highlighting two distinct oligomerization interfaces: the (N-terminal domain [NTD] and C-terminal domain [CTD]) in mVP40. Cellular studies of NTD and CTD oligomerization interface mutants demonstrate the importance of each interface in matrix assembly. The assembly steps include protein trafficking to the plasma membrane, homo-multimerization that induced protein enrichment, plasma membrane fluidity changes, and elongations at the plasma membrane. An ascorbate peroxidase derivative (APEX)-transmission electron microscopy method was employed to closely assess the ultrastructural localization and formation of viral particles for wildtype mVP40 and NTD and CTD oligomerization interface mutants. Taken together, these studies present a mechanistic model of mVP40 oligomerization and assembly at the plasma membrane during virion assembly that requires interactions with phosphatidylserine for NTD–NTD interactions and phosphatidylinositol-4,5-bisphosphate for proper CTD–CTD interactions. These findings have broader implications in understanding budding of lipid-enveloped viruses from the host cell plasma membrane and potential strategies to target protein–protein or lipid–protein interactions to inhibit virus budding.
Collapse
Affiliation(s)
- Souad Amiar
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Monica L Husby
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Kaveesha J Wijesinghe
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Stephanie Angel
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA.
| |
Collapse
|
34
|
Winter SL, Chlanda P. Dual-axis Volta phase plate cryo-electron tomography of Ebola virus-like particles reveals actin-VP40 interactions. J Struct Biol 2021; 213:107742. [PMID: 33971285 DOI: 10.1016/j.jsb.2021.107742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/17/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
Cryo-electron tomography (cryo-ET) is a pivotal imaging technique for studying the structure of pleomorphic enveloped viruses and their interactions with the host at native conditions. Owing to the limited tilting range of samples with a slab geometry, electron tomograms suffer from so-called missing wedge information in Fourier space. In dual-axis cryo-ET, two tomograms reconstructed from orthogonally oriented tilt series are combined into a tomogram with improved resolution as the missing wedge information is reduced to a pyramid. Volta phase plate (VPP) allows to perform in-focus cryo-ET with high contrast transfer at low-resolution frequencies and thus its application may improve the quality of dual-axis tomograms. Here, we compare dual-axis cryo-ET with and without VPP on Ebola virus-like particles to visualize and segment viral and host cell proteins within the membrane-enveloped filamentous particles. Dual-axis VPP cryo-ET reduces the missing wedge information and ray artifacts arising from the weighted back-projection during tomogram reconstruction, thereby minimizing ambiguity in the analysis of crowded environments and facilitating 3D segmentation. We show that dual-axis VPP tomograms provide a comprehensive description of macromolecular organizations such as nucleocapsid assembly states, the distribution of glycoproteins on the viral envelope and asymmetric arrangements of the VP40 layer in non-filamentous regions of virus-like particles. Our data reveal actin filaments within virus-like particles in close proximity to the viral VP40 scaffold, suggesting a direct interaction between VP40 and actin filaments. Dual-axis VPP cryo-ET provides more complete 3D information at high contrast and allows for better interpretation of macromolecule interactions and pleomorphic organizations.
Collapse
Affiliation(s)
- Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; Research Group "Membrane Biology of Viral Infection", Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; Research Group "Membrane Biology of Viral Infection", Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|
35
|
[The latest research findings on Ebola virus]. Uirusu 2021; 71:137-150. [PMID: 37245976 DOI: 10.2222/jsv.71.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
013-2016 Ebola virus disease (EVD) outbreak was the largest EVD outbreak ever documented that started earlier in Guinea and later widely spread throughout West Africa, ending up a total of > 28,000 human infections. In this review, we outline research findings on Ebola virus (EBOV) variant Makona, a new EBOV variant isolated from the 2013-2016 EVD outbreak, and introduce the unique biological and pathogenic characteristics of Makona variant. We also discuss about the relevance of persistent infection of EBOV in EVD survivors with resurgence of EVD outbreak in Guinea in 2021. Moreover, this review covers a recent case report of EVD relapse and deliberates new interpretations of EBOV biology and EVD outbreak.
Collapse
|