1
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Tresset G, Li S, Gargowitsch L, Matthews L, Pérez J, Zandi R. Glass-like Relaxation Dynamics during the Disorder-to-Order Transition of Viral Nucleocapsids. J Phys Chem Lett 2024:10210-10218. [PMID: 39356145 DOI: 10.1021/acs.jpclett.4c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Nucleocapsid self-assembly is an essential yet elusive step in virus replication. Using time-resolved small-angle X-ray scattering on a model icosahedral ssRNA virus, we reveal a previously unreported kinetic pathway. Initially, RNA-bound capsid subunits rapidly accumulate beyond the stoichiometry of native virions. This is followed by a disorder-to-order transition characterized by glass-like relaxation dynamics and the release of excess subunits. Our molecular dynamics simulations, employing a coarse-grained elastic model, confirm the physical feasibility of self-ordering accompanied by subunit release. The relaxation can be modeled by an exponential integral decay on the mean squared radius of gyration, with relaxation times varying within the second range depending on RNA type and subunit concentration. A nanogel model suggests that the initially disordered nucleoprotein complexes quickly reach an equilibrium size, while their mass fractal dimension continues to evolve. Understanding virus self-assembly is not only crucial for combating viral infections, but also for designing synthetic virus-inspired nanocages for drug delivery applications.
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Affiliation(s)
- Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | | | - Javier Pérez
- SOLEIL Synchrotron, 91192 Gif-sur-Yvette, France
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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2
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Wroblewski E, Patel N, Javed A, Mata CP, Chandler-Bostock R, Lekshmi BG, Ulamec SM, Clark S, Phillips SEV, Ranson NA, Twarock R, Stockley PG. Visualizing Viral RNA Packaging Signals in Action. J Mol Biol 2024; 436:168765. [PMID: 39214281 DOI: 10.1016/j.jmb.2024.168765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5' two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T = 1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5' PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3' end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.
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Affiliation(s)
- Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Abid Javed
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rebecca Chandler-Bostock
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - B G Lekshmi
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom
| | - Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sam Clark
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom
| | - Simon E V Phillips
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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3
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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [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: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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4
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Hori M, Steinauer A, Tetter S, Hälg J, Manz EM, Hilvert D. Stimulus-responsive assembly of nonviral nucleocapsids. Nat Commun 2024; 15:3576. [PMID: 38678040 PMCID: PMC11055949 DOI: 10.1038/s41467-024-47808-1] [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: 02/17/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
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Affiliation(s)
- Mao Hori
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LIBN, Lausanne, Switzerland
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jamiro Hälg
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Eva-Maria Manz
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
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5
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Ramirez-Acosta K, Loredo-García E, Herrera-Hernandez MM, Cadena-Nava RD. Plant Virus-Like Particles for RNA Delivery. Methods Mol Biol 2024; 2822:387-410. [PMID: 38907930 DOI: 10.1007/978-1-0716-3918-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Plant viruses such as brome mosaic virus and cowpea chlorotic mottle virus are effectively purified through PEG precipitation and sucrose cushion ultracentrifugation. Increasing ionic strength and an alkaline pH cause the viruses to swell and disassemble into coat protein subunits. The coat proteins can be reassembled into stable virus-like particles (VLPs) that carry anionic molecules at low ionic strength and through two-step dialysis from neutral pH to acidic buffer. VLPs have been extensively studied due to their ability to protect and deliver cargo, particularly RNA, while avoiding degradation under physiological conditions. Furthermore, chemical functionalization of the surface of VLPs allows for the targeted drug delivery. VLPs derived from plants have demonstrated great potential in nanomedicine by offering a versatile platform for drug delivery, imaging, and therapeutic applications.
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Affiliation(s)
- Kendra Ramirez-Acosta
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - Elizabeth Loredo-García
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - M Mariana Herrera-Hernandez
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, Mexico
| | - Ruben D Cadena-Nava
- Centro de Nanociencias y Nanotecnología-Universidad Nacional Autónoma de México (UNAM), Ensenada, Baja California, Mexico.
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6
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Asor R, Singaram SW, Levi-Kalisman Y, Hagan MF, Raviv U. Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate). THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:107. [PMID: 37917241 DOI: 10.1140/epje/s10189-023-00363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
Abstract
Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent, such as RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with a combinatorial number of intermediates. Hence, the mechanism of the reaction is poorly understood. In this paper, we combined solution small-angle X-ray scattering (SAXS), cryo-transmission electron microscopy (TEM), and computational modeling to determine the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by SAXS and cryo-TEM. To analyze the data, we performed Langevin dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures consistent with the experimental data. We found that close to physiological ionic strength, [Formula: see text] VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and [Formula: see text] particles. Including the simulated structures was essential to explain the SAXS data in a manner that is consistent with the cryo-TEM images.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Surendra W Singaram
- Department of Physics, Brandeis University, 415 South Street, Waltham, 02453, MA, USA
| | - Yael Levi-Kalisman
- Institute of Life Sciences and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Michael F Hagan
- Department of Physics, Brandeis University, 415 South Street, Waltham, 02453, MA, USA.
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel.
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7
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González-Davis O, Villagrana-Escareño MV, Trujillo MA, Gama P, Chauhan K, Vazquez-Duhalt R. Virus-like nanoparticles as enzyme carriers for Enzyme Replacement Therapy (ERT). Virology 2023; 580:73-87. [PMID: 36791560 DOI: 10.1016/j.virol.2023.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023]
Abstract
Enzyme replacement therapy (ERT) has been used to treat a few of the many existing diseases which are originated from the lack of, or low enzymatic activity. Exogenous enzymes are administered to contend with the enzymatic activity deficiency. Enzymatic nanoreactors based on the enzyme encapsulation inside of virus-like particles (VLPs) appear as an interesting alternative for ERT. VLPs are excellent delivery vehicles for therapeutic enzymes as they are biodegradable, uniformly organized, and porous nanostructures that transport and could protect the biocatalyst from the external environment without much affecting the bioactivity. Consequently, significant efforts have been made in the production processes of virus-based enzymatic nanoreactors and their functionalization, which are critically reviewed. The use of virus-based enzymatic nanoreactors for the treatment of lysosomal storage diseases such as Gaucher, Fabry, and Pompe diseases, as well as potential therapies for galactosemia, and Hurler and Hunter syndromes are discussed.
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Affiliation(s)
- Oscar González-Davis
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera, Tijuana-Ensenada, Baja California, 22860, Mexico
| | - Maria V Villagrana-Escareño
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera, Tijuana-Ensenada, Baja California, 22860, Mexico
| | - Mario A Trujillo
- School of Medicine, Universidad Xochicalco, Ensenada, Baja California, Mexico
| | - Pedro Gama
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera, Tijuana-Ensenada, Baja California, 22860, Mexico
| | - Kanchan Chauhan
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera, Tijuana-Ensenada, Baja California, 22860, Mexico
| | - Rafael Vazquez-Duhalt
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera, Tijuana-Ensenada, Baja California, 22860, Mexico.
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8
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Switalski K, Fan J, Li L, Chu M, Sarnello E, Jemian P, Li T, Wang Q, Zhang Q. Direct measurement of Stokes-Einstein diffusion of Cowpea mosaic virus with 19 µs-resolved XPCS. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1429-1435. [PMID: 36345751 PMCID: PMC9641563 DOI: 10.1107/s1600577522008402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Brownian motion of Cowpea mosaic virus (CPMV) in water was measured using small-angle X-ray photon correlation spectroscopy (SA-XPCS) at 19.2 µs time resolution. It was found that the decorrelation time τ(Q) = 1/DQ2 up to Q = 0.091 nm-1. The hydrodynamic radius RH determined from XPCS using Stokes-Einstein diffusion D = kT/(6πηRH) is 43% larger than the geometric radius R0 determined from SAXS in the 0.007 M K3PO4 buffer solution, whereas it is 80% larger for CPMV in 0.5 M NaCl and 104% larger in 0.5 M (NH4)2SO4, a possible effect of aggregation as well as slight variation of the structures of the capsid resulting from the salt-protein interactions.
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Affiliation(s)
- Kacper Switalski
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60611, USA
| | - Jingyu Fan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Luxi Li
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Miaoqi Chu
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Erik Sarnello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Pete Jemian
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Tao Li
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Qingteng Zhang
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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9
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Mizrahi I, Bruinsma R, Rudnick J. Spanning tree model and the assembly kinetics of RNA viruses. Phys Rev E 2022; 106:044405. [PMID: 36397584 DOI: 10.1103/physreve.106.044405] [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: 08/09/2021] [Accepted: 05/17/2022] [Indexed: 06/16/2023]
Abstract
Single-stranded RNA (ssRNA) viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules and it is not known whether this also can be understood by free energy minimization. We address this question using a simple mathematical model, the spanning tree model, that was recently proposed for the assembly of small ssRNA viruses. We present a statistical physics analysis of the properties of this model. RNA selection takes place via a kinetic mechanism that operates during the formation of the nucleation complex and that is related to Hopfield kinetic proofreading.
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Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
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10
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Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles. Proc Natl Acad Sci U S A 2022; 119:e2206292119. [PMID: 36122222 PMCID: PMC9522328 DOI: 10.1073/pnas.2206292119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Understanding the pathways by which simple RNA viruses self-assemble from their coat proteins and RNA is of practical and fundamental interest. Although RNA-protein interactions are thought to play a critical role in the assembly, our understanding of their effects is limited because the assembly process is difficult to observe directly. We address this problem by using interferometric scattering microscopy, a sensitive optical technique with high dynamic range, to follow the in vitro assembly kinetics of more than 500 individual particles of brome mosaic virus (BMV)-for which RNA-protein interactions can be controlled by varying the ionic strength of the buffer. We find that when RNA-protein interactions are weak, BMV assembles by a nucleation-and-growth pathway in which a small cluster of RNA-bound proteins must exceed a critical size before additional proteins can bind. As the strength of RNA-protein interactions increases, the nucleation time becomes shorter and more narrowly distributed, but the time to grow a capsid after nucleation is largely unaffected. These results suggest that the nucleation rate is controlled by RNA-protein interactions, while the growth process is driven less by RNA-protein interactions and more by protein-protein interactions and intraprotein forces. The nucleated pathway observed with the plant virus BMV is strikingly similar to that previously observed with bacteriophage MS2, a phylogenetically distinct virus with a different host kingdom. These results raise the possibility that nucleated assembly pathways might be common to other RNA viruses.
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11
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Cooper CD, Addison-Smith I, Guzman HV. Quantitative electrostatic force tomography for virus capsids in interaction with an approaching nanoscale probe. NANOSCALE 2022; 14:12232-12237. [PMID: 35975473 DOI: 10.1039/d2nr02526d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Electrostatic interactions are crucial for the assembly, disassembly and stability of proteinaceous viral capsids. Moreover, at the molecular scale, elucidating the organization and structure of the capsid proteins in response to an approaching nanoprobe is a major challenge in biomacromolecular research. Here, we report on a generalized electrostatic model, based on the Poisson-Boltzmann equation, that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid from molecular snapshots. This allows us to describe the contributions of specific amino acids and atoms to the interaction force. We show validation results in terms of total electrostatic forces with previous semi-empirical generalized models at available length scales (d > 1 nm). Then, we studied the interaction of the Zika capsid with conical and spherical AFM tips in a tomography-type analysis to identify the most important residues and atoms, showing the localized nature of the interaction. This method can be employed for the interpretation of force microscopy experiments in fundamental virological characterization and in diverse nanomedicine applications, where specific regions of the protein cages are aimed to electrostatically interact with molecular sized functionalized inhibitors, or tailoring protein-cage functional properties for nucleic acid delivery.
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Affiliation(s)
- Christopher D Cooper
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
- Centro Científico Tecnológico de Valparaíso (CCTVal), 2390123 Valparaíso, Chile
| | - Ian Addison-Smith
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
| | - Horacio V Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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12
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Almendárez-Rodriguez C, Solis-Andrade KI, Govea-Alonso DO, Comas-Garcia M, Rosales-Mendoza S. Production and characterization of chimeric SARS-CoV-2 antigens based on the capsid protein of cowpea chlorotic mottle virus. Int J Biol Macromol 2022; 213:1007-1017. [PMID: 35690161 PMCID: PMC9174154 DOI: 10.1016/j.ijbiomac.2022.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022]
Abstract
The COVID-19 pandemic has highlighted the need for new vaccine platforms to rapidly develop solutions against emerging pathogens. In particular, some plant viruses offer several advantages for developing subunit vaccines, such as high expression rates in E. coli, high immunogenicity and safety, and absence of pre-immunity that could interfere with the vaccine's efficacy. Cowpea chlorotic mottle virus (CCMV) is a model system that has been extensively characterized, with key advantages for its use as an epitope carrier. In the present study, three relevant epitopes from the SARS-CoV-2 Spike protein were genetically inserted into the CCMV CP and expressed in E. coli cultures, resulting in the CCMV1, CCMV2, and CCMV3 chimeras. The recombinant CP mutants were purified from the formed inclusion bodies and refolded, and their immunogenicity as a subunit vaccine was assessed in BALB/c mice. The three mutants are immunogenic as they induce high IgG antibody titers that recognize the recombinant full-length S protein. This study supports the application of CCMV CP as an attractive carrier for the clinical evaluation of vaccine candidates against SARS-CoV-2. Furthermore, it suggests that VLPs assembled from these chimeric proteins could result in antigens with better immunogenicity.
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Affiliation(s)
- Claudia Almendárez-Rodriguez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Karla I Solis-Andrade
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Dania O Govea-Alonso
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico
| | - Mauricio Comas-Garcia
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico; Sección de Microscopía de Alta Resolución, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico; Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Parque Chapultepec 1570, 78210 San Luis, S.L.P., San Luis Potosí 78210, Mexico.
| | - Sergio Rosales-Mendoza
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, Mexico.
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13
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Harati Taji Z, Bielytskyi P, Shein M, Sani MA, Seitz S, Schütz AK. Transient RNA Interactions Leave a Covalent Imprint on a Viral Capsid Protein. J Am Chem Soc 2022; 144:8536-8550. [PMID: 35512333 PMCID: PMC9121876 DOI: 10.1021/jacs.1c12439] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The hepatitis B virus (HBV) is the leading cause of persistent liver infections. Its DNA-based genome is synthesized through reverse transcription of an RNA template inside the assembled capsid shell. In addition to the structured assembly domain, the capsid protein harbors a C-terminal extension that mediates both the enclosure of RNA during capsid assembly and the nuclear entry of the capsid during infection. The arginine-rich motifs within this extension, though common to many viruses, have largely escaped atomic-scale investigation. Here, we leverage solution and solid-state nuclear magnetic resonance spectroscopy at ambient and cryogenic temperatures, under dynamic nuclear polarization signal enhancement, to investigate the organization of the genome within the capsid. Transient interactions with phosphate groups of the RNA backbone confine the arginine-rich motifs to the interior capsid space. While no secondary structure is induced in the C-terminal extension, interactions with RNA counteract the formation of a disulfide bond, which covalently tethers this peptide arm onto the inner capsid surface. Electrostatic and covalent contributions thus compete in the spatial regulation of capsid architecture. This disulfide switch represents a coupling mechanism between the structured assembly domain of the capsid and the enclosed nucleic acids. In particular, it enables the redox-dependent regulation of the exposure of the C-terminal extension on the capsid surface, which is required for nuclear uptake of the capsid. Phylogenetic analysis of capsid proteins from hepadnaviruses points toward a function of this switch in the persistence of HBV infections.
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Affiliation(s)
- Zahra Harati Taji
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching 85748, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Pavlo Bielytskyi
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching 85748, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching 85748, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Stefan Seitz
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg 69120, Germany.,Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Anne K Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching 85748, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
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14
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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15
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Mizrahi I, Bruinsma R, Rudnick J. Packaging contests between viral RNA molecules and kinetic selectivity. PLoS Comput Biol 2022; 18:e1009913. [PMID: 35363785 PMCID: PMC9022832 DOI: 10.1371/journal.pcbi.1009913] [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: 08/15/2021] [Revised: 04/21/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules by packaging signals during the nucleation stage of the assembly of small RNA viruses. The effects of the RNA secondary structure and folding geometry of the packaging signals on the assembly activation energy barrier are encoded by a pair of characteristics: the wrapping number and the maximum ladder distance. Kinetic selection is found to be optimal when assembly takes place under conditions of supersaturation and also when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. As a function of the height of the activation energy barrier, there is a form of order-disorder transition such that for sufficiently low activation energy barriers, kinetic selectivity is erased by entropic effects associated with the number of assembly pathways.
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Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- * E-mail:
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
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16
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Ruszkowski M, Strugala A, Indyka P, Tresset G, Figlerowicz M, Urbanowicz A. Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure. NANOSCALE 2022; 14:3224-3233. [PMID: 35156989 DOI: 10.1039/d1nr05650f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features de novo. In this paper, we describe VLPs assembled in vitro from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified VLPs.
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Affiliation(s)
- Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Aleksander Strugala
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Paulina Indyka
- Jagiellonian University, Solaris National Synchrotron Radiation Centre, Czerwone Maki 98, 30-392 Cracow, Poland
- Jagiellonian University, Malopolska Centre of Biotechnology (MCB), 30-387 Cracow, Poland
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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17
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Patel N, Clark S, Weiß EU, Mata CP, Bohon J, Farquhar ER, Maskell DP, Ranson NA, Twarock R, Stockley PG. In vitro functional analysis of gRNA sites regulating assembly of hepatitis B virus. Commun Biol 2021; 4:1407. [PMID: 34916604 PMCID: PMC8677749 DOI: 10.1038/s42003-021-02897-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The roles of RNA sequence/structure motifs, Packaging Signals (PSs), for regulating assembly of an HBV genome transcript have been investigated in an efficient in vitro assay containing only core protein (Cp) and RNA. Variants of three conserved PSs, within the genome of a strain not used previously, preventing correct presentation of a Cp-recognition loop motif are differentially deleterious for assembly of nucleocapsid-like particles (NCPs). Cryo-electron microscopy reconstruction of the T = 4 NCPs formed with the wild-type gRNA transcript, reveal that the interior of the Cp shell is in contact with lower resolution density, potentially encompassing the arginine-rich protein domains and gRNA. Symmetry relaxation followed by asymmetric reconstruction reveal that such contacts are made at every symmetry axis. We infer from their regulation of assembly that some of these contacts would involve gRNA PSs, and confirmed this by X-ray RNA footprinting. Mutation of the ε stem-loop in the gRNA, where polymerase binds in vivo, produces a poor RNA assembly substrate with Cp alone, largely due to alterations in its conformation. The results show that RNA PSs regulate assembly of HBV genomic transcripts in vitro, and therefore may play similar roles in vivo, in concert with other molecular factors.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sam Clark
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Eva U Weiß
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Electron and Confocal Microscopy Unit (UCCTs), National Centre for Microbiology (ISCIII). Majadahonda, Madrid, Spain
| | - Jen Bohon
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Erik R Farquhar
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Reidun Twarock
- Departments of Biology and Mathematics & York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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18
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Barnes LF, Draper BE, Chen YT, Powers TW, Jarrold MF. Quantitative analysis of genome packaging in recombinant AAV vectors by charge detection mass spectrometry. Mol Ther Methods Clin Dev 2021; 23:87-97. [PMID: 34631929 PMCID: PMC8476707 DOI: 10.1016/j.omtm.2021.08.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has emerged as an important gene therapy vector with many clinical trials currently in progress. Analytical characterization and quantitation of particle content remain challenges in both the development and production of rAAV vectors. In this study, charge detection mass spectrometry (CDMS) and gel electrophoresis are used to characterize the DNA content of recombinant AAV8 (rAAV8) vectors with a wide range of target genome sizes. We show that the differences between the masses of empty particles and particles with the genome of interest (GOI) are correlated with the expected genome mass. A small systematic deviation (around 2%) is attributed to the packaging of counterions along with the DNA. In addition to the GOI, a broad distribution of heterogeneous DNA is packaged. The distribution peaks are close to the packaging capacity of the rAAV8 vectors. There is also evidence for the co-packaging of small DNA fragments along with the GOI. Finally, we present evidence that incubation at an elevated temperature can reduce the heterogeneity of the packaged DNA. Taken together, these results show that CDMS is a viable tool for characterization of the packaged genome.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Benjamin E Draper
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Yu-Ting Chen
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Thomas W Powers
- Pfizer, Inc., BioTherapeutics Pharmaceutical Sciences, Analytical R&D, 875 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
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19
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Poblete S, Božič A, Kanduč M, Podgornik R, Guzman HV. RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates. ACS OMEGA 2021; 6:32823-32831. [PMID: 34901632 PMCID: PMC8655909 DOI: 10.1021/acsomega.1c04774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
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Affiliation(s)
- Simón Poblete
- Instituto
de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Computational
Biology Lab, Fundación Ciencia &
Vida, Santiago 7780272, Chile
| | - Anže Božič
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Matej Kanduč
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- School
of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Horacio V. Guzman
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
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20
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Marichal L, Gargowitsch L, Rubim RL, Sizun C, Kra K, Bressanelli S, Dong Y, Panahandeh S, Zandi R, Tresset G. Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus. Biophys J 2021; 120:3925-3936. [PMID: 34418368 PMCID: PMC8511167 DOI: 10.1016/j.bpj.2021.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/21/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
The process of genome packaging in most of viruses is poorly understood, notably the role of the genome itself in the nucleocapsid structure. For simple icosahedral single-stranded RNA viruses, the branched topology due to the RNA secondary structure is thought to lower the free energy required to complete a virion. We investigate the structure of nucleocapsids packaging RNA segments with various degrees of compactness by small-angle x-ray scattering and cryotransmission electron microscopy. The structural differences are mild even though compact RNA segments lead on average to better-ordered and more uniform particles across the sample. Numerical calculations confirm that the free energy is lowered for the RNA segments displaying the larger number of branch points. The effect is, however, opposite with synthetic polyelectrolytes, in which a star topology gives rise to more disorder in the capsids than a linear topology. If RNA compactness and size account in part for the proper assembly of the nucleocapsid and the genome selectivity, other factors most likely related to the host cell environment during viral assembly must come into play as well.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Laetitia Gargowitsch
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Rafael Leite Rubim
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Christina Sizun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Kalouna Kra
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Yinan Dong
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France.
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21
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Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021; 13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Affiliation(s)
- Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
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22
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Hill SR, Twarock R, Dykeman EC. The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus. PLoS Comput Biol 2021; 17:e1009306. [PMID: 34428224 PMCID: PMC8384211 DOI: 10.1371/journal.pcbi.1009306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro.
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Affiliation(s)
- Sam R. Hill
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Eric C. Dykeman
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
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23
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Zeng C, Scott L, Malyutin A, Zandi R, Van der Schoot P, Dragnea B. Virus Mechanics under Molecular Crowding. J Phys Chem B 2021; 125:1790-1798. [PMID: 33577322 DOI: 10.1021/acs.jpcb.0c10947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viruses avoid exposure of the viral genome to harmful agents with the help of a protective protein shell known as the capsid. A secondary effect of this protective barrier is that macromolecules that may be in high concentration on the outside cannot freely diffuse across it. Therefore, inside the cell and possibly even outside, the intact virus is generally under a state of osmotic stress. Viruses deal with this type of stress in various ways. In some cases, they might harness it for infection. However, the magnitude and influence of osmotic stress on virus physical properties remains virtually unexplored for single-stranded RNA viruses-the most abundant class of viruses. Here, we report on how a model system for the positive-sense RNA icosahedral viruses, brome mosaic virus (BMV), responds to osmotic pressure. Specifically, we study the mechanical properties and structural stability of BMV under controlled molecular crowding conditions. We show that BMV is mechanically reinforced under a small external osmotic pressure but starts to yield after a threshold pressure is reached. We explain this mechanochemical behavior as an effect of the molecular crowding on the entropy of the "breathing" fluctuation modes of the virus shell. The experimental results are consistent with the viral RNA imposing a small negative internal osmotic pressure that prestresses the capsid. Our findings add a new line of inquiry to be considered when addressing the mechanisms of viral disassembly inside the crowded environment of the cell.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Liam Scott
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Andrey Malyutin
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, Riverside, California 92521, United States
| | | | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Bloomington, Indiana 47405, United States
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24
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Chan SK, Du P, Ignacio C, Mehta S, Newton IG, Steinmetz NF. Biomimetic Virus-Like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools. ACS NANO 2021; 15:1259-1272. [PMID: 33237727 PMCID: PMC7724985 DOI: 10.1021/acsnano.0c08430] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible disease that has affected more than 90% of the countries worldwide. At least 17 million individuals have been infected, and some countries are still battling first or second waves of the pandemic. Nucleic acid tests, especially reverse transcription polymerase chain reaction (RT-PCR), have become the workhorse for early detection of COVID-19 infection. Positive controls for the molecular assays have been developed to validate each test and to provide high accuracy. However, most available positive controls require cold-chain distribution and cannot serve as full-process control. To overcome these shortcomings, we report the production of biomimetic virus-like particles (VLPs) as SARS-CoV-2 positive controls. A SARS-CoV-2 detection module for RT-PCR was encapsidated into VLPs from a bacteriophage and a plant virus. The chimeric VLPs were obtained either by in vivo reconstitution and coexpression of the target detection module and coat proteins or by in vitro assembly of purified detection module RNA sequences and coat proteins. These VLP-based positive controls mimic SARS-CoV-2 packaged ribonucleic acid (RNA) while being noninfectious. Most importantly, we demonstrated that the positive controls are scalable, stable, and can serve broadly as controls, from RNA extraction to PCR in clinical settings.
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Affiliation(s)
- Soo Khim Chan
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Pinyi Du
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Caroline Ignacio
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Sanjay Mehta
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Isabel G. Newton
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
| | - Nicole F. Steinmetz
- Department of NanoEngineering,
Department of Medicine,
Department of Radiology,
Department of Bioengineering,
Center for Nano-ImmunoEngineering,
Moores Cancer Center, Institute for
Materials Discovery and Design, and Veterans
Administration San Diego Healthcare System, University of
California San Diego, 9500 Gilman Drive, La Jolla,
California 92039, United States
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25
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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26
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Bond K, Tsvetkova IB, Wang JCY, Jarrold MF, Dragnea B. Virus Assembly Pathways: Straying Away but Not Too Far. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004475. [PMID: 33241653 DOI: 10.1002/smll.202004475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native one. However, they contain large native structure fragments that can be recycled to form BMV virions, should a viral genome become available. The existence of such structures suggest the possibility of a previously unknown regulatory pathway for the packaging process inside cells.
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Affiliation(s)
- Kevin Bond
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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27
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Vervoort DFM, Pretto C, van Hest JCM. Insight into N-terminal localization and dynamics of engineered virus-like particles. RSC Adv 2020; 10:38774-38781. [PMID: 35518386 PMCID: PMC9057346 DOI: 10.1039/d0ra07612k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles composed of the cowpea chlorotic mottle virus (CCMV) capsid protein (CP) have been extensively studied as carrier systems in nanoscience. One well-established method to improve their stability under physiological conditions is to fuse a stimulus-responsive elastin-like polypeptide (ELP) to the N-terminus of the CPs. Even though the N-terminus should in principle be localized in the inner cavity of the protein cage, studies on the native CCMV revealed its accessibility on the particle surface. We verified that such phenomenon also applies to ELP-CCMVs, by exploiting the covalent functionalization of the CP N-terminal domain via a sortase A-mediated reaction. Western-blot analysis and Förster resonance energy transfer (FRET) experiments furthermore revealed this to be caused by both the external display of the N-termini and the interchange of CPs among preformed capsids. Our findings demonstrate the tunability of ELP-CCMV stability and dynamics and their potential effect on the exploitation of such protein cages as a drug delivery system.
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Affiliation(s)
- Daan F M Vervoort
- Eindhoven University of Technology, Institute for Complex Molecular Systems PO Box 513 (STO 3.41) 5600 MB Eindhoven The Netherlands
| | - Chiara Pretto
- Eindhoven University of Technology, Institute for Complex Molecular Systems PO Box 513 (STO 3.41) 5600 MB Eindhoven The Netherlands
| | - Jan C M van Hest
- Eindhoven University of Technology, Institute for Complex Molecular Systems PO Box 513 (STO 3.41) 5600 MB Eindhoven The Netherlands
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28
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Perspectives on Viral RNA Genomes and the RNA Folding Problem. Viruses 2020; 12:v12101126. [PMID: 33027988 PMCID: PMC7600889 DOI: 10.3390/v12101126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles. These structurally dynamic RNA shapeshifters present a challenging RNA folding problem, because the RNA sequence adopts multiple structures and may sometimes contain regions of partial disorder. Recent advances in high resolution asymmetric cryoelectron microscopy and chemical probing provide new ways to probe the degree of structure and disorder, and have identified more than one conformation in dynamic equilibrium in viral RNA. Chemical probing and the Detection of RNA Folding Ensembles using Expectation Maximization (DREEM) algorithm has been applied to studies of the dynamic equilibrium conformations in HIV RNA in vitro, in virio, and in vivo. This new type of data provides insight into important questions about virus assembly mechanisms and the fundamental physical forces driving virus particle assembly.
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29
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Poon WCK, Brown AT, Direito SOL, Hodgson DJM, Le Nagard L, Lips A, MacPhee CE, Marenduzzo D, Royer JR, Silva AF, Thijssen JHJ, Titmuss S. Soft matter science and the COVID-19 pandemic. SOFT MATTER 2020; 16:8310-8324. [PMID: 32909024 DOI: 10.1039/d0sm01223h] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes controls their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. We survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.
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Affiliation(s)
- Wilson C K Poon
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Aidan T Brown
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Susana O L Direito
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Daniel J M Hodgson
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Lucas Le Nagard
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Alex Lips
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Cait E MacPhee
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Davide Marenduzzo
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - John R Royer
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Andreia F Silva
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Job H J Thijssen
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Simon Titmuss
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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30
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Schlicksup CJ, Zlotnick A. Viral structural proteins as targets for antivirals. Curr Opin Virol 2020; 45:43-50. [PMID: 32777753 DOI: 10.1016/j.coviro.2020.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/29/2022]
Abstract
Viral structural proteins are emerging as effective targets for new antivirals. In a viral lifecycle, the capsid must assemble, disassemble, and respond to host proteins, all at the right time and place. These reactions work within a narrow range of conditions, making them susceptible to small molecule interference. In at least three specific viruses, this approach has had met with preliminary success. In rhinovirus and poliovirus, compounds like pleconaril bind capsid and block RNA release. Bevirimat binds to Gag protein in HIV, inhibiting maturation. In Hepatitis B virus, core protein allosteric modulators (CpAMs) promote spontaneous assembly of capsid protein leading to empty and aberrant particles. Despite the biological diversity between viruses and the chemical diversity between antiviral molecules, we observe common features in these antivirals' mechanisms of action. These approaches work by stabilizing protein-protein interactions.
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Affiliation(s)
- Christopher John Schlicksup
- Molecular and Cellular Biology Department, Indiana University-Bloomington, Bloomington, IN 47401, United States
| | - Adam Zlotnick
- Molecular and Cellular Biology Department, Indiana University-Bloomington, Bloomington, IN 47401, United States.
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31
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Fu J, Woycechowsky KJ. Guest Sequence Can Influence RNA Encapsulation by an Engineered Cationic Protein Capsid. Biochemistry 2020; 59:1517-1526. [DOI: 10.1021/acs.biochem.0c00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiannan Fu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
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32
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Ni R, Chau Y. Nanoassembly of Oligopeptides and DNA Mimics the Sequential Disassembly of a Spherical Virus. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201913611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong Ni
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
| | - Ying Chau
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
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33
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Ni R, Chau Y. Nanoassembly of Oligopeptides and DNA Mimics the Sequential Disassembly of a Spherical Virus. Angew Chem Int Ed Engl 2019; 59:3578-3584. [DOI: 10.1002/anie.201913611] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Rong Ni
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
| | - Ying Chau
- Department of Chemical and Biological EngineeringThe Hong Kong University of Science and Technology Clearwater Bay Kowloon, Hong Kong China
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34
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Pretto C, van Hest JCM. Versatile Reversible Cross-Linking Strategy to Stabilize CCMV Virus Like Particles for Efficient siRNA Delivery. Bioconjug Chem 2019; 30:3069-3077. [PMID: 31765129 PMCID: PMC6923791 DOI: 10.1021/acs.bioconjchem.9b00731] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Virus like particles obtained from the Cowpea Chlorotic
Mottle
Virus (CCMV) represent an innovative platform for drug delivery applications.
Their unique reversible self-assembly properties as well as their
suitability for both cargo loading and functionalization make them
a versatile scaffold for numerous purposes. One of the main drawbacks
of this platform is however its limited stability at physiological
conditions. Herein, we report the development of a general reversible
cross-linking strategy involving the homobifunctional cross-linker
DTSSP (3,3′-dithiobis (sulfosuccinimidylpropionate)) which
is suitable for particle stabilization. This methodology is adaptable
to different CCMV variants in the presence or absence of a stabilizing
cargo without varying neither particle shape nor size thus extending
the potential use of these protein cages in nanomedical applications.
Cross-linked particles are stable at neutral pH and 37 °C and
they are capable of protecting loaded cargo against enzymatic digestion.
Furthermore, the reversible nature of the cross-linking ensures particle
disassembly when they are taken up by cells. This was demonstrated
via the highly effective delivery of active siRNA into cells.
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Affiliation(s)
- Chiara Pretto
- Eindhoven University of Technology , Institute for Complex Molecular Systems , PO Box 513, 5600 MB Eindhoven , The Netherlands
| | - Jan C M van Hest
- Eindhoven University of Technology , Institute for Complex Molecular Systems , PO Box 513, 5600 MB Eindhoven , The Netherlands
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35
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Maassen SJ, Huskens J, Cornelissen JJLM. Elucidating the Thermodynamic Driving Forces of Polyanion-Templated Virus-like Particle Assembly. J Phys Chem B 2019; 123:9733-9741. [PMID: 31661278 PMCID: PMC6875872 DOI: 10.1021/acs.jpcb.9b06258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/01/2019] [Indexed: 01/09/2023]
Abstract
A virus in its most simple form is comprised of a protein capsid that surrounds and protects the viral genome. The self-assembly of such structures, however, is a highly complex, multiprotein, multiinteraction process and has been a topic of study for a number of years. This self-assembly process is driven by the (mainly electrostatic) interaction between the capsid proteins (CPs) and the genome as well as by the protein-protein interactions, which primarily rely on hydrophobic interactions. Insight in the thermodynamics that is involved in virus and virus-like particle (VLP) formation is crucial in the detailed understanding of this complex assembly process. Therefore, we studied the assembly of CPs of the cowpea chlorotic mottle virus (CCMV) templated by polyanionic species (cargo), that is, single-stranded DNA (ssDNA), and polystyrene sulfonate (PSS) using isothermal titration calorimetry. By separating the electrostatic CP-cargo interaction from the full assembly interaction, we conclude that CP-CP interactions cause an enthalpy change of -3 to -4 kcal mol-1 CP. Furthermore, we quantify that upon reducing the CP-CP interaction, in the case of CCMV by increasing the pH to 7, the CP-cargo starts to dominate VLP formation. This is highlighted by the three times higher affinity between CP and PSS compared to CP and ssDNA, resulting in the disassembly of CCMV at neutral pH in the presence of PSS to yield PSS-filled VLPs.
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Affiliation(s)
- Stan J. Maassen
- Laboratory
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology and Molecular NanoFabrication
Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede 7500 AE, The Netherlands
| | - Jurriaan Huskens
- Laboratory
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology and Molecular NanoFabrication
Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede 7500 AE, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Laboratory
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology and Molecular NanoFabrication
Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede 7500 AE, The Netherlands
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36
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Villagrana-Escareño MV, Reynaga-Hernández E, Galicia-Cruz OG, Durán-Meza AL, De la Cruz-González V, Hernández-Carballo CY, Ruíz-García J. VLPs Derived from the CCMV Plant Virus Can Directly Transfect and Deliver Heterologous Genes for Translation into Mammalian Cells. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4630891. [PMID: 31781617 PMCID: PMC6855080 DOI: 10.1155/2019/4630891] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
Abstract
Virus-like particles (VLPs) are being used for therapeutic developments such as vaccines and drug nanocarriers. Among these, plant virus capsids are gaining interest for the formation of VLPs because they can be safely handled and are noncytotoxic. A paradigm in virology, however, is that plant viruses cannot transfect and deliver directly their genetic material or other cargos into mammalian cells. In this work, we prepared VLPs with the CCMV capsid and the mRNA-EGFP as a cargo and reporter gene. We show, for the first time, that these plant virus-based VLPs are capable of directly transfecting different eukaryotic cell lines, without the aid of any transfecting adjuvant, and delivering their nucleic acid for translation as observed by the presence of fluorescent protein. Our results show that the CCMV capsid is a good noncytotoxic container for genome delivery into mammalian cells.
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Affiliation(s)
- María V. Villagrana-Escareño
- Physical Biology Laboratory, Institute of Physics, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
| | - Elizabeth Reynaga-Hernández
- Physical Biology Laboratory, Institute of Physics, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
| | - Othir G. Galicia-Cruz
- Analytical Pharmacology Laboratory, Faculty of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
| | - Ana L. Durán-Meza
- Physical Biology Laboratory, Institute of Physics, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
| | - Viridiana De la Cruz-González
- Physical Biology Laboratory, Institute of Physics, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
| | | | - Jaime Ruíz-García
- Physical Biology Laboratory, Institute of Physics, Autonomous University of San Luis Potosí, San Luis Potosí, Mexico
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37
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Edwardson TGW, Hilvert D. Virus-Inspired Function in Engineered Protein Cages. J Am Chem Soc 2019; 141:9432-9443. [PMID: 31117660 DOI: 10.1021/jacs.9b03705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structural and functional diversity of proteins combined with their genetic programmability has made them indispensable modern materials. Well-defined, hollow protein capsules have proven to be particularly useful due to their ability to compartmentalize macromolecules and chemical processes. To this end, viral capsids are common scaffolds and have been successfully repurposed to produce a suite of practical protein-based nanotechnologies. Recently, the recapitulation of viromimetic function in protein cages of nonviral origin has emerged as a strategy to both complement physical studies of natural viruses and produce useful scaffolds for diverse applications. In this perspective, we review recent progress toward generation of virus-like behavior in nonviral protein cages through rational engineering and directed evolution. These artificial systems can aid our understanding of the emergence of viruses from existing cellular components, as well as provide alternative approaches to tackle current problems, and open up new opportunities, in medicine and biotechnology.
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Affiliation(s)
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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38
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Biddlecome A, Habte HH, McGrath KM, Sambanthamoorthy S, Wurm M, Sykora MM, Knobler CM, Lorenz IC, Lasaro M, Elbers K, Gelbart WM. Delivery of self-amplifying RNA vaccines in in vitro reconstituted virus-like particles. PLoS One 2019; 14:e0215031. [PMID: 31163034 PMCID: PMC6548422 DOI: 10.1371/journal.pone.0215031] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/25/2019] [Indexed: 01/01/2023] Open
Abstract
Many mRNA-based vaccines have been investigated for their specific potential to activate dendritic cells (DCs), the highly-specialized antigen-presenting cells of the immune system that play a key role in inducing effective CD4+ and CD8+ T-cell responses. In this paper we report a new vaccine/gene delivery platform that demonstrates the benefits of using a self-amplifying (“replicon”) mRNA that is protected in a viral-protein capsid. Purified capsid protein from the plant virus Cowpea Chlorotic Mottle Virus (CCMV) is used to in vitro assemble monodisperse virus-like particles (VLPs) containing reporter proteins (e.g., Luciferase or eYFP) or the tandem-repeat model antigen SIINFEKL in RNA gene form, coupled to the RNA-dependent RNA polymerase from the Nodamura insect virus. Incubation of immature DCs with these VLPs results in increased activation of maturation markers – CD80, CD86 and MHC-II – and enhanced RNA replication levels, relative to incubation with unpackaged replicon mRNA. Higher RNA uptake/replication and enhanced DC activation were detected in a dose-dependent manner when the CCMV-VLPs were pre-incubated with anti-CCMV antibodies. In all experiments the expression of maturation markers correlates with the RNA levels of the DCs. Overall, these studies demonstrate that: VLP protection enhances mRNA uptake by DCs; coupling replicons to the gene of interest increases RNA and protein levels in the cell; and the presence of anti-VLP antibodies enhances mRNA levels and activation of DCs in vitro. Finally, preliminary in vivo experiments involving mouse vaccinations with SIINFEKL-replicon VLPs indicate a small but significant increase in antigen-specific T cells that are doubly positive for IFN and TFN induction.
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Affiliation(s)
- Adam Biddlecome
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
| | - Habtom H. Habte
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, United States of America
| | - Katherine M. McGrath
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, United States of America
| | | | - Melanie Wurm
- Boehringer-Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Charles M. Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
| | - Ivo C. Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - Marcio Lasaro
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, United States of America
| | - Knut Elbers
- Boehringer-Ingelheim Pharma GmbH & Co KG, Biberach, Germany
- * E-mail: (KE); (WMG)
| | - William M. Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- * E-mail: (KE); (WMG)
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39
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Comas-Garcia M. Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story. Viruses 2019; 11:v11030253. [PMID: 30871184 PMCID: PMC6466141 DOI: 10.3390/v11030253] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.
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Affiliation(s)
- Mauricio Comas-Garcia
- Research Center for Health Sciences and Biomedicine (CICSaB), Universidad Autónoma de San Luis Potosí (UASLP), Av. Sierra Leona 550 Lomas 2da Seccion, 72810 San Luis Potosi, Mexico.
- Department of Sciences, Universidad Autónoma de San Luis Potosí (UASLP), Av. Chapultepec 1570, Privadas del Pedregal, 78295 San Luis Potosi, Mexico.
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40
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Garmann RF, Knobler CM, Gelbart WM. Protocol for Efficient Cell-Free Synthesis of Cowpea Chlorotic Mottle Virus-Like Particles Containing Heterologous RNAs. Methods Mol Biol 2019; 1776:249-265. [PMID: 29869247 DOI: 10.1007/978-1-4939-7808-3_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a protocol for efficient cell-free synthesis of cowpea chlorotic mottle virus (CCMV)-like particles containing a broad range of lengths and sequences of RNA. Our protocol starts with a purified stock of wild-type CCMV (protocols for harvesting and purifying the virus are detailed elsewhere) and features three basic steps: disassembly of the CCMV and purification of the capsid protein (CP) from the viral RNA; coassembly of the purified CP and an RNA of choice; and characterization of the assembly products. We highlight several key factors that increase the yield of the assembly reaction: the CP should be uncleaved and sufficiently free of viral RNA; the length of the RNA should be between about 100 and 4000 nucleotides; and the stoichiometry of CP and RNA should be 6-1 by mass. Additionally, we point out that separating the assembly reaction into multiple steps-by successively lowering the ionic strength and then the pH of the assembly buffers-results in the highest yields of well-formed, nuclease-resistant, CCMV-like particles. Finally, we describe methods for characterizing the assembly products using native agarose gel electrophoresis and negative-stain transmission electron microscopy.
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Affiliation(s)
- Rees F Garmann
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, USA
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41
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Maassen SJ, van der Schoot P, Cornelissen JJLM. Experimental and Theoretical Determination of the pH inside the Confinement of a Virus-Like Particle. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802081. [PMID: 30102454 DOI: 10.1002/smll.201802081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/17/2018] [Indexed: 06/08/2023]
Abstract
In biology, a variety of highly ordered nanometer-size protein cages is found. Such structures find increasing application in, for example, vaccination, drug delivery, and catalysis. Understanding the physiochemical properties, particularly inside the confinement of a protein cage, helps to predict the behavior and properties of new materials based on such particles. Here, the relation between the bulk solution pH and the local pH inside a model protein cage, based on virus-like particles (VLPs) built from the coat proteins of the cowpea chlorotic mottle virus, is investigated. The pH is a crucial parameter in a variety of processes and is potentially significantly influenced by the high concentration of charges residing on the interior of the VLPs. The data show a systematic more acidic pH of 0.5 unit inside the VLP compared to that of the bulk solution for pH values above pH 6, which is explained using a theoretical model based on a Donnan equilibrium. The model agrees with the experimental data over almost two orders of magnitude, while below pH 6 the experimental data point to a buffering capacity of the VLP. These results are a first step in a better understanding of the physiochemical conditions inside a protein cage.
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Affiliation(s)
- Stan J Maassen
- Laboratory of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, Enschede, 7500, AE, The Netherlands
| | - Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, The Netherlands
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584, CC, Utrecht, The Netherlands
| | - Jeroen J L M Cornelissen
- Laboratory of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, Enschede, 7500, AE, The Netherlands
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42
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Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte. Nat Commun 2018; 9:3071. [PMID: 30082710 PMCID: PMC6078970 DOI: 10.1038/s41467-018-05426-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/05/2018] [Indexed: 11/20/2022] Open
Abstract
The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape. The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements.
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43
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Twarock R, Bingham RJ, Dykeman EC, Stockley PG. A modelling paradigm for RNA virus assembly. Curr Opin Virol 2018; 31:74-81. [PMID: 30078702 PMCID: PMC6281560 DOI: 10.1016/j.coviro.2018.07.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022]
Abstract
Virus assembly, a key stage in any viral life cycle, had long been considered to be primarily driven by protein-protein interactions and nonspecific interactions between genomic RNA and capsid protein. We review here a modelling paradigm for RNA virus assembly that illustrates the crucial roles of multiple dispersed, specific interactions between viral genomes and coat proteins in capsid assembly. The model reveals how multiple sequence-structure motifs in the genomic RNA, termed packaging signals, with a shared coat protein recognition motif enable viruses to overcome a viral assembly-equivalent of Levinthal's Paradox in protein folding. The fitness advantages conferred by this mechanism suggest that it should be widespread in viruses, opening up new perspectives on viral evolution and anti-viral therapy.
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Affiliation(s)
- Reidun Twarock
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5NG, UK.
| | - Richard J Bingham
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5NG, UK
| | - Eric C Dykeman
- York Centre for Cross-disciplinary Systems Analysis, University of York, York YO10 5GE, UK; Department of Mathematics, University of York, York YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT UK
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44
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Systematic analysis of biological roles of charged amino acid residues located throughout the structured inner wall of a virus capsid. Sci Rep 2018; 8:9543. [PMID: 29934575 PMCID: PMC6015035 DOI: 10.1038/s41598-018-27749-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
Structure-based mutational analysis of viruses is providing many insights into the relationship between structure and biological function of macromolecular complexes. We have systematically investigated the individual biological roles of charged residues located throughout the structured capsid inner wall (outside disordered peptide segments) of a model spherical virus, the minute virus of mice (MVM). The functional effects of point mutations that altered the electrical charge at 16 different positions at the capsid inner wall were analyzed. The results revealed that MVM capsid self-assembly is rather tolerant to point mutations that alter the number and distribution of charged residues at the capsid inner wall. However, mutations that either increased or decreased the number of positive charges around capsid-bound DNA segments reduced the thermal resistance of the virion. Moreover, mutations that either removed or changed the positions of negatively charged carboxylates in rings of acidic residues around capsid pores were deleterious by precluding a capsid conformational transition associated to through-pore translocation events. The results suggest that number, distribution and specific position of electrically charged residues across the inner wall of a spherical virus may have been selected through evolution as a compromise between several different biological requirements.
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45
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Maassen SJ, de Ruiter MV, Lindhoud S, Cornelissen JJLM. Oligonucleotide Length-Dependent Formation of Virus-Like Particles. Chemistry 2018. [PMID: 29518273 DOI: 10.1002/chem.201800285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Understanding the assembly pathway of viruses can contribute to creating monodisperse virus-based materials. In this study, the cowpea chlorotic mottle virus (CCMV) is used to determine the interactions between the capsid proteins of viruses and their cargo. The assembly of the capsid proteins in the presence of different lengths of short, single-stranded (ss) DNA is studied at neutral pH, at which the protein-protein interactions are weak. Chromatography, electrophoresis, microscopy, and light scattering data show that the assembly efficiency and speed of the particles increase with increasing length of oligonucleotides. The minimal length required for assembly under the conditions used herein is 14 nucleotides. Assembly of particles containing such short strands of ssDNA can take almost a month. This slow assembly process enabled the study of intermediate states, which confirmed a low cooperative assembly for CCMV and allowed for further expansion of current assembly theories.
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Affiliation(s)
- Stan J Maassen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Saskia Lindhoud
- Department of Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Jeroen J L M Cornelissen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
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46
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van der Holst B, Kegel WK, Zandi R, van der Schoot P. The different faces of mass action in virus assembly. J Biol Phys 2018; 44:163-179. [PMID: 29616429 PMCID: PMC5928020 DOI: 10.1007/s10867-018-9487-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation. By invoking mass action-type arguments and a simple model describing electrostatic interactions, we show how these forms of entropy might settle the competition between negatively charged polymers of different molecular weights for co-assembly with the coat proteins. In direct competition, mass action turns out to strongly work against the encapsulation of RNAs that are significantly shorter, which is typically the case for non-viral (host) RNAs. We also find that coat proteins favor forming virus particles over nonspecific binding to other proteins in the cytosol even if these are present in vast excess. Our results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.
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Affiliation(s)
- Bart van der Holst
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Willem K Kegel
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands. .,Institute for Theoretical Physics, Utrecht University, Utrecht, The Netherlands.
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47
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Lošdorfer Božič A, Podgornik R. Varieties of charge distributions in coat proteins of ssRNA+ viruses. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:024001. [PMID: 29182522 PMCID: PMC7104810 DOI: 10.1088/1361-648x/aa9ded] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+ viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that-in contrast to the charge on the CPs-the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.
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Affiliation(s)
- Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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48
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Azuma Y, Edwardson TGW, Terasaka N, Hilvert D. Modular Protein Cages for Size-Selective RNA Packaging in Vivo. J Am Chem Soc 2018; 140:566-569. [DOI: 10.1021/jacs.7b10798] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Naohiro Terasaka
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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49
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Rayaprolu V, Moore A, Wang JCY, Goh BC, Perilla JR, Zlotnick A, Mukhopadhyay S. Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:484003. [PMID: 28975896 PMCID: PMC7103146 DOI: 10.1088/1361-648x/aa90d0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/28/2017] [Accepted: 10/04/2017] [Indexed: 05/21/2023]
Abstract
In vitro assembly of alphavirus nucleocapsid cores, called core-like particles (CLPs), requires a polyanionic cargo. There are no sequence or structure requirements to encapsidate single-stranded nucleic acid cargo. In this work, we wanted to determine how the length of the cargo impacts the stability and structure of the assembled CLPs. We hypothesized that cargo neutralizes the basic region of the alphavirus capsid protein and if the cargo is long enough, it will also act to scaffold the CP monomers together. Experimentally we found that CLPs encapsidating short 27mer oligonucleotides were less stable than CLPs encapsidating 48mer or 90mer oligonucleotides under different chemical and thermal conditions. Furthermore, cryo-EM studies showed there were structural differences between CLPs assembled with 27mer and 48mer cargo. To mimic the role of the cargo in CLP assembly we made a mutant (4D) where we substituted a cluster of four Lys residues in the CP with four Asp residues. We found that these few amino acid substitutions were enough to initiate CLP assembly in the absence of cargo. The cargo-free 4D CLPs show higher resistance to ionic strength and increased temperature compared to wild-type cargo containing CLPs suggesting their CLP assembly mechanism might also be different.
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Affiliation(s)
- Vamseedhar Rayaprolu
- Departments of Biology, Indiana University, Bloomington, IN, United States of America
| | - Alan Moore
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, United States of America
| | - Joseph Che-Yen Wang
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, United States of America
| | - Boon Chong Goh
- Physics and Beckman Institute, University of Illinois Urbana-Champaign, Champaign, IL, United States of America
| | - Juan R Perilla
- Physics and Beckman Institute, University of Illinois Urbana-Champaign, Champaign, IL, United States of America
- Center of Physics for Living Cells, University of Illinois Urbana-Champaign, Champaign, IL, United States of America
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, United States of America
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50
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Patel N, Wroblewski E, Leonov G, Phillips SEV, Tuma R, Twarock R, Stockley PG. Rewriting nature's assembly manual for a ssRNA virus. Proc Natl Acad Sci U S A 2017; 114:12255-12260. [PMID: 29087310 PMCID: PMC5699041 DOI: 10.1073/pnas.1706951114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Satellite tobacco necrosis virus (STNV) is one of the smallest viruses known. Its genome encodes only its coat protein (CP) subunit, relying on the polymerase of its helper virus TNV for replication. The genome has been shown to contain a cryptic set of dispersed assembly signals in the form of stem-loops that each present a minimal CP-binding motif AXXA in the loops. The genomic fragment encompassing nucleotides 1-127 is predicted to contain five such packaging signals (PSs). We have used mutagenesis to determine the critical assembly features in this region. These include the CP-binding motif, the relative placement of PS stem-loops, their number, and their folding propensity. CP binding has an electrostatic contribution, but assembly nucleation is dominated by the recognition of the folded PSs in the RNA fragment. Mutation to remove all AXXA motifs in PSs throughout the genome yields an RNA that is unable to assemble efficiently. In contrast, when a synthetic 127-nt fragment encompassing improved PSs is swapped onto the RNA otherwise lacking CP recognition motifs, assembly is partially restored, although the virus-like particles created are incomplete, implying that PSs outside this region are required for correct assembly. Swapping this improved region into the wild-type STNV1 sequence results in a better assembly substrate than the viral RNA, producing complete capsids and outcompeting the wild-type genome in head-to-head competition. These data confirm details of the PS-mediated assembly mechanism for STNV and identify an efficient approach for production of stable virus-like particles encapsidating nonnative RNAs or other cargoes.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - German Leonov
- York Centre for Complex Systems Analysis, University of York, Heslington, York YO10 5DD, United Kingdom
- Department of Mathematics, University of York, Heslington, York YO10 5DD, United Kingdom
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Simon E V Phillips
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, OX11 0FA, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, Heslington, York YO10 5DD, United Kingdom
- Department of Mathematics, University of York, Heslington, York YO10 5DD, United Kingdom
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
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