1
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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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2
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Brown C, Agarwal A, Luque A. pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells. Bioinformatics 2024; 40:btad761. [PMID: 38113434 PMCID: PMC10786678 DOI: 10.1093/bioinformatics/btad761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/01/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023] Open
Abstract
SUMMARY pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. AVAILABILITY AND IMPLEMENTATION pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.
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Affiliation(s)
- Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Department of Physics, San Diego State University, San Diego, CA 92116, United States
| | - Anuradha Agarwal
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, United States
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
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3
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Jablunovsky A, Narayanan A, Jose J. Identification of a critical role for ZIKV capsid α3 in virus assembly and its genetic interaction with M protein. PLoS Negl Trop Dis 2024; 18:e0011873. [PMID: 38166143 PMCID: PMC10786401 DOI: 10.1371/journal.pntd.0011873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/12/2024] [Accepted: 12/19/2023] [Indexed: 01/04/2024] Open
Abstract
Flaviviruses such as Zika and dengue viruses are persistent health concerns in endemic regions worldwide. Efforts to combat the spread of flaviviruses have been challenging, as no antivirals or optimal vaccines are available. Prevention and treatment of flavivirus-induced diseases require a comprehensive understanding of their life cycle. However, several aspects of flavivirus biogenesis, including genome packaging and virion assembly, are not well characterized. In this study, we focused on flavivirus capsid protein (C) using Zika virus (ZIKV) as a model to investigate the role of the externally oriented α3 helix (C α3) without a known or predicted function. Alanine scanning mutagenesis of surface-exposed amino acids on C α3 revealed a critical CN67 residue essential for ZIKV virion production. The CN67A mutation did not affect dimerization or RNA binding of purified C protein in vitro. The virus assembly is severely affected in cells transfected with an infectious cDNA clone of ZIKV with CN67A mutation, resulting in a highly attenuated phenotype. We isolated a revertant virus with a partially restored phenotype by continuous passage of the CN67A mutant virus in Vero E6 cells. Sequence analysis of the revertant revealed a second site mutation in the viral membrane (M) protein MF37L, indicating a genetic interaction between the C and M proteins of ZIKV. Introducing the MF37L mutation on the mutant ZIKV CN67A generated a double-mutant virus phenotypically consistent with the isolated genetic revertant. Similar results were obtained with analogous mutations on C and M proteins of dengue virus, suggesting the critical nature of C α3 and possible C and M residues contributing to virus assembly in other Aedes-transmitted flaviviruses. This study provides the first experimental evidence of a genetic interaction between the C protein and the viral envelope protein M, providing a mechanistic understanding of the molecular interactions involved in the assembly and budding of Aedes-transmitted flaviviruses.
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Affiliation(s)
- Anastazia Jablunovsky
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Anoop Narayanan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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4
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Twarock R, Towers GJ, Stockley PG. Molecular frustration: a hypothesis for regulation of viral infections. Trends Microbiol 2024; 32:17-26. [PMID: 37507296 DOI: 10.1016/j.tim.2023.07.003] [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: 11/30/2022] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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5
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Butkovic A, Dolja VV, Koonin EV, Krupovic M. Plant virus movement proteins originated from jelly-roll capsid proteins. PLoS Biol 2023; 21:e3002157. [PMID: 37319262 DOI: 10.1371/journal.pbio.3002157] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Numerous, diverse plant viruses encode movement proteins (MPs) that aid the virus movement through plasmodesmata, the plant intercellular channels. MPs are essential for virus spread and propagation in distal tissues, and several unrelated MPs have been identified. The 30K superfamily of MPs (named after the molecular mass of tobacco mosaic virus (TMV) MP, the classical model of plant virology) is the largest and most diverse MP variety, represented in 16 virus families, but its evolutionary origin remained obscure. Here, we show that the core structural domain of the 30K MPs is homologous to the jelly-roll domain of the capsid proteins (CPs) of small RNA and DNA viruses, in particular, those infecting plants. The closest similarity was observed between the 30K MPs and the CPs of the viruses in the families Bromoviridae and Geminiviridae. We hypothesize that the MPs evolved via duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants, followed by neofunctionalization of one of the paralogous CPs, potentially through the acquisition of unique N- and C-terminal regions. During the subsequent coevolution of viruses with diversifying vascular plants, the 30K MP genes underwent explosive horizontal spread among emergent RNA and DNA viruses, likely permitting viruses of insects and fungi that coinfected plants to expand their host ranges, molding the contemporary plant virome.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
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6
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Ranjan T, Ranjan Kumar R, Ansar M, Kumar J, Mohanty A, Kumari A, Jain K, Rajani K, Dei S, Ahmad MF. The curious case of genome packaging and assembly in RNA viruses infecting plants. Front Genet 2023; 14:1198647. [PMID: 37359368 PMCID: PMC10285054 DOI: 10.3389/fgene.2023.1198647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Genome packaging is the crucial step for maturation of plant viruses containing an RNA genome. Viruses exhibit a remarkable degree of packaging specificity, despite the probability of co-packaging cellular RNAs. Three different types of viral genome packaging systems are reported so far. The recently upgraded type I genome packaging system involves nucleation and encapsidation of RNA genomes in an energy-dependent manner, which have been observed in most of the plant RNA viruses with a smaller genome size, while type II and III packaging systems, majorly discovered in bacteriophages and large eukaryotic DNA viruses, involve genome translocation and packaging inside the prohead in an energy-dependent manner, i.e., utilizing ATP. Although ATP is essential for all three packaging systems, each machinery system employs a unique mode of ATP hydrolysis and genome packaging mechanism. Plant RNA viruses are serious threats to agricultural and horticultural crops and account for huge economic losses. Developing control strategies against plant RNA viruses requires a deep understanding of their genome assembly and packaging mechanism. On the basis of our previous studies and meticulously planned experiments, we have revealed their molecular mechanisms and proposed a hypothetical model for the type I packaging system with an emphasis on smaller plant RNA viruses. Here, in this review, we apprise researchers the technical breakthroughs that have facilitated the dissection of genome packaging and virion assembly processes in plant RNA viruses.
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Affiliation(s)
- Tushar Ranjan
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Ravi Ranjan Kumar
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Mohammad Ansar
- Department of Plant Pathology, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Jitesh Kumar
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Auroshikha Mohanty
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Anamika Kumari
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Khushbu Jain
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Kumari Rajani
- Department of Seed Science and Technology, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Sailabala Dei
- Deputy Director Research, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Mohammad Feza Ahmad
- Department of Horticulture, Bihar Agricultural University, Bhagalpur, Bihar, India
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7
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van der Meulen K, Smets G, Rüdelsheim P. Viral Replicon Systems and Their Biosafety Aspects. APPLIED BIOSAFETY 2023; 28:102-122. [PMID: 37342518 PMCID: PMC10278005 DOI: 10.1089/apb.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Introduction Viral RNA replicons are self-amplifying RNA molecules generated by deleting genetic information of one or multiple structural proteins of wild-type viruses. Remaining viral RNA is used as such (naked replicon) or packaged into a viral replicon particle (VRP), whereby missing genes or proteins are supplied via production cells. Since replicons mostly originate from pathogenic wild-type viruses, careful risk consideration is crucial. Methods A literature review was performed compiling information on potential biosafety risks of replicons originating from positive- and negative-sense single-stranded RNA viruses (except retroviruses). Results For naked replicons, risk considerations included genome integration, persistence in host cells, generation of virus-like vesicles, and off-target effects. For VRP, the main risk consideration was formation of primary replication competent virus (RCV) as a result of recombination or complementation. To limit the risks, mostly measures aiming at reducing the likelihood of RCV formation have been described. Also, modifying viral proteins in such a way that they do not exhibit hazardous characteristics in the unlikely event of RCV formation has been reported. Discussion and Conclusion Despite multiple approaches developed to reduce the likelihood of RCV formation, scientific uncertainty remains on the actual contribution of the measures and on limitations to test their effectiveness. In contrast, even though effectiveness of each individual measure is unclear, using multiple measures on different aspects of the system may create a solid barrier. Risk considerations identified in the current study can also be used to support risk group assignment of replicon constructs based on a purely synthetic design.
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8
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Zagrovic B, Adlhart M, Kapral TH. Coding From Binding? Molecular Interactions at the Heart of Translation. Annu Rev Biophys 2023; 52:69-89. [PMID: 36626765 DOI: 10.1146/annurev-biophys-090622-102329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs & University of Vienna, Vienna, Austria;
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
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9
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Fuertes MA, López Mateos D, Valiente L, Rodríguez Huete A, Valbuena A, Mateu MG. Electrostatic Screening, Acidic pH and Macromolecular Crowding Increase the Self-Assembly Efficiency of the Minute Virus of Mice Capsid In Vitro. Viruses 2023; 15:v15051054. [PMID: 37243141 DOI: 10.3390/v15051054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
The hollow protein capsids from a number of different viruses are being considered for multiple biomedical or nanotechnological applications. In order to improve the applied potential of a given viral capsid as a nanocarrier or nanocontainer, specific conditions must be found for achieving its faithful and efficient assembly in vitro. The small size, adequate physical properties and specialized biological functions of the capsids of parvoviruses such as the minute virus of mice (MVM) make them excellent choices as nanocarriers and nanocontainers. In this study we analyzed the effects of protein concentration, macromolecular crowding, temperature, pH, ionic strength, or a combination of some of those variables on the fidelity and efficiency of self-assembly of the MVM capsid in vitro. The results revealed that the in vitro reassembly of the MVM capsid is an efficient and faithful process. Under some conditions, up to ~40% of the starting virus capsids were reassembled in vitro as free, non aggregated, correctly assembled particles. These results open up the possibility of encapsidating different compounds in VP2-only capsids of MVM during its reassembly in vitro, and encourage the use of virus-like particles of MVM as nanocontainers.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Diego López Mateos
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez Huete
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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10
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Ortega-Rivera OA, Beiss V, Osota EO, Chan SK, Karan S, Steinmetz NF. Production of cytoplasmic type citrus leprosis virus-like particles by plant molecular farming. Virology 2023; 578:7-12. [PMID: 36434906 PMCID: PMC9812895 DOI: 10.1016/j.virol.2022.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Many plant virus-like particles (VLPs) utilized in nanotechnology are 30-nm icosahedrons. To expand the VLP platforms, we produced VLPs of Cytoplasmic type citrus leprosis virus (CiLV-C) in Nicotiana benthamiana. We were interested in CiLV-C because of its unique bacilliform shape (60-70 nm × 110-120 nm). The CiLV-C capsid protein (p29) gene was transferred to the pTRBO expression vector transiently expressed in leaves. Stable VLPs were formed, as confirmed by agarose gel electrophoresis, transmission electron microscopy and size exclusion chromatography. Interestingly, the morphology of the VLPs (15.8 ± 1.3 nm icosahedral particles) differed from that of the native bacilliform particles indicating that the assembly of native virions is influenced by other viral proteins and/or the packaged viral genome. The smaller CiLV-C VLPs will also be useful for structure-function studies to compare with the 30-nm icosahedrons of other VLPs.
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Affiliation(s)
- Oscar A Ortega-Rivera
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA
| | - Veronique Beiss
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA
| | - Elizabeth O Osota
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA
| | - Soo Khim Chan
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA
| | - Sweta Karan
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Center for Nano-ImmunoEngineering, University of California-San Diego, La Jolla, CA, 92039, USA; Institute for Materials Discovery and Design, University of California-San Diego, La Jolla, CA, 92039, USA; Department of Bioengineering, University of California-San Diego, La Jolla, CA, 92039, USA; Department of Radiology, University of California-San Diego, La Jolla, CA, 92039, USA; Moores Cancer Center, University of California-San Diego, La Jolla, CA, 92039, USA.
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11
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Saunders K, Thuenemann EC, Peyret H, Lomonossoff GP. The Tobacco Mosaic Virus Origin of Assembly Sequence is Dispensable for Specific Viral RNA Encapsidation but Necessary for Initiating Assembly at a Single Site. J Mol Biol 2022; 434:167873. [PMID: 36328231 DOI: 10.1016/j.jmb.2022.167873] [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: 08/23/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
We have investigated whether the presence of the origin of assembly sequence (OAS) of tobacco mosaic virus (TMV) is necessary for the specific encapsidation of replicating viral RNA. To this end TMV coat protein was expressed from replicating RNA constructs with or without the OAS in planta. In both cases the replicating RNA was specifically encapsidated to give nucleoprotein nanorods, though the yield in the absence of the OAS was reduced to about 60% of that in its presence. Moreover, the nanorods generated in the absence of the OAS were more heterogeneous in length and contained frequent structural discontinuities. These results strongly suggest that the function of the OAS is to provide a unique site for the initiation of viral assembly, leading to a one-start helix, rather than the selection of virus RNA for packaging.
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Affiliation(s)
- Keith Saunders
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eva C Thuenemann
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hadrien Peyret
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - George P Lomonossoff
- Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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12
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Rolband L, Beasock D, Wang Y, Shu YG, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Šulc P, Binzel D, Bhullar AS, Liang C, Guo P, Afonin KA. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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Affiliation(s)
- Lewis Rolband
- University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Damian Beasock
- University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Yang Wang
- Wenzhou Institute, University of China Academy of Sciences, 1st, Jinlian Road, Longwan District, Wenzhou, Zhjiang 325001, China
| | - Yao-Gen Shu
- Wenzhou Institute, University of China Academy of Sciences, 1st, Jinlian Road, Longwan District, Wenzhou, Zhjiang 325001, China
| | | | - Tamar Schlick
- New York University, Department of Chemistry and Courant Institute of Mathematical Sciences, Simons Center for Computational Physical Chemistry, New York, NY 10012, USA
| | - Yaoqi Zhou
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518107, China
| | - Jeffrey S. Kieft
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shi-Jie Chen
- University of Missouri at Columbia, Columbia, MO 65211, USA
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | | | - Xingfa Gao
- National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Petr Šulc
- Arizona State University, Tempe, AZ, USA
| | | | | | - Chenxi Liang
- The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- The Ohio State University, Columbus, OH 43210, USA
| | - Kirill A. Afonin
- University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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13
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Chandler-Bostock R, Bingham RJ, Clark S, Scott AJP, Wroblewski E, Barker A, White SJ, Dykeman EC, Mata CP, Bohon J, Farquhar E, Twarock R, Stockley PG. Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection. J Mol Biol 2022; 434:167797. [PMID: 35998704 DOI: 10.1016/j.jmb.2022.167797] [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: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former. This is also true for a virus-like particle (VLP) assembled around the gRNA in vitro in the absence of the single-copy Maturation Protein (MP) found in phage. Since PS folds are present at many sites across gRNA transcripts, it appears that this genome has evolved to facilitate this mechanism of assembly regulation. There are striking differences between the gRNA-CP contacts seen in phage and the VLP, suggesting that the latter are inappropriate surrogates for aspects of phage structure/function. Roughly 50% of potential PS sites in the gRNA are not in contact with the protein shell of phage. However, many of these sit adjacent to, albeit not in contact with, PS-binding sites on CP dimers. We hypothesize that these act as PSs transiently during assembly but subsequently dissociate. Combining the XRF data with PS locations from an asymmetric cryo-EM reconstruction suggests that the genome positions of such dissociations are non-random and may facilitate infection. The loss of many PS-CP interactions towards the 3' end of the gRNA would allow this part of the genome to transit more easily through the narrow basal body of the pilus extruding machinery. This is the known first step in phage infection. In addition, each PS-CP dissociation event leaves the protein partner trapped in a non-lowest free-energy conformation. This destabilizes the protein shell which must disassemble during infection, further facilitating this stage of the life-cycle.
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Affiliation(s)
| | - Richard J Bingham
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Sam Clark
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy Barker
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eric C Dykeman
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jen Bohon
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Erik Farquhar
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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14
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Patel N, Abulwerdi F, Fatehi F, Manfield IW, Le Grice S, Schneekloth JS, Twarock R, Stockley PG. Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands. J Mol Biol 2022; 434:167557. [PMID: 35341740 PMCID: PMC7612645 DOI: 10.1016/j.jmb.2022.167557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022]
Abstract
RNA sequences/motifs dispersed across the genome of Hepatitis B Virus regulate formation of nucleocapsid-like particles (NCPs) by core protein (Cp) in vitro, in an epsilon/polymerase-independent fashion. These multiple RNA Packaging Signals (PSs) can each form stem-loops encompassing a Cp-recognition motif, -RGAG-, in their loops. Drug-like molecules that bind the most important of these PS sites for NCP assembly regulation with nanomolar affinities, were identified by screening an immobilized ligand library with a fluorescently-labelled, RNA oligonucleotide encompassing this sequence. Sixty-six of these "hits", with affinities ranging from low nanomolar to high micromolar, were purchased as non-immobilized versions. Their affinities for PSs and effects on NCP assembly were determined in vitro by Surface Plasmon Resonance. High-affinity ligand binding is dependent on the presence of an -RGAG- motif within the loop of the PS, consistent with ligand cross-binding between PS sites. Simple structure-activity relationships show that it is also dependent on the presence of specific functional groups in these ligands. Some compounds are potent inhibitors of in vitro NCP assembly at nanomolar concentrations. Despite appropriate logP values, these ligands do not inhibit HBV replication in cell culture. However, modelling confirms the potential of using PS-binding ligands to target NCP assembly as a novel anti-viral strategy. This also allows for computational exploration of potential synergic effects between anti-viral ligands directed at distinct molecular targets in vivo. HBV PS-regulated assembly can be dysregulated by novel small molecule RNA-binding ligands opening a novel target for developing directly-acting anti-virals against this major pathogen.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/FBSResearch
| | - Fardokht Abulwerdi
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stuart Le Grice
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - John S Schneekloth
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Reidun Twarock
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK; Department of Biology, University of York, York, YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/AstburyCentre
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15
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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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16
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Adlhart M, Poetsch F, Hlevnjak M, Hoogmoed M, Polyansky A, Zagrovic B. Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses. Nucleic Acids Res 2022; 50:4054-4067. [PMID: 35357492 PMCID: PMC9023274 DOI: 10.1093/nar/gkac202] [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: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 02/02/2023] Open
Abstract
During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.
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Affiliation(s)
- Marlene Adlhart
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Florian Poetsch
- Institute for Physiology and Pathophysiology, Center for Medical Research, Johannes Kepler University of Linz, Huemerstraße 3-5, 4020 Linz, Austria
| | - Mario Hlevnjak
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Megan Hoogmoed
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria
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17
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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18
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Biela AP, Naskalska A, Fatehi F, Twarock R, Heddle JG. Programmable polymorphism of a virus-like particle. COMMUNICATIONS MATERIALS 2022; 3:7. [PMID: 35284827 PMCID: PMC7612486 DOI: 10.1038/s43246-022-00229-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled polymorphism using a single protein subunit is challenging as it requires altering VLP geometry. Here we achieve size control of MS2 bacteriophage VLPs via insertion of amino acid sequences in an external loop to shift morphology to significantly larger forms. The resulting VLP size and geometry is controlled by altering the length and type of the insert. Cryo electron microscopy structures of the new VLPs, in combination with a kinetic model of their assembly, show that the abundance of wild type (T = 3), T = 4, D3 and D5 symmetrical VLPs can be biased in this way. We propose a mechanism whereby the insert leads to a change in the dynamic behavior of the capsid protein dimer, affecting the interconversion between the symmetric and asymmetric conformers and thus determining VLP size and morphology.
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Affiliation(s)
- Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Antonina Naskalska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Farzad Fatehi
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
| | - Reidun Twarock
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
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19
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Abstract
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatics interaction between the positive charges on capsid proteins and the negative charges on the genome. Despite its importance and many decades of intense research, how the virus selects and packages its native RNA inside the crowded environment of a host cell cytoplasm in the presence of an abundance of nonviral RNA and other anionic polymers has remained a mystery. In this paper, we perform a series of simulations to monitor the growth of viral shells and find the mechanism by which cargo-coat protein interactions can impact the structure and stability of the viral shells. We show that coat protein subunits can assemble around a globular nucleic acid core by forming nonicosahedral cages, which have been recently observed in assembly experiments involving small pieces of RNA. We find that the resulting cages are strained and can easily be split into fragments along stress lines. This suggests that such metastable nonicosahedral intermediates could be easily reassembled into the stable native icosahedral shells if the larger wild-type genome becomes available, despite the presence of a myriad of nonviral RNAs.
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Affiliation(s)
- Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Siyu Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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20
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An age-structured model of hepatitis B viral infection highlights the potential of different therapeutic strategies. Sci Rep 2022; 12:1252. [PMID: 35075156 PMCID: PMC8786976 DOI: 10.1038/s41598-021-04022-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatitis B virus (HBV) is a global health threat, and its elimination by 2030 has been prioritised by the World Health Organisation. Here we present an age-structured model for the immune response to an HBV infection, which takes into account contributions from both cell-mediated and humoral immunity. The model has been validated using published patient data recorded during acute infection. It has been adapted to the scenarios of chronic infection, clearance of infection, and flare-ups via variation of the immune response parameters. The impacts of immune response exhaustion and non-infectious subviral particles on the immune response dynamics are analysed. A comparison of different treatment options in the context of this model reveals that drugs targeting aspects of the viral life cycle are more effective than exhaustion therapy, a form of therapy mitigating immune response exhaustion. Our results suggest that antiviral treatment is best started when viral load is declining rather than in a flare-up. The model suggests that a fast antibody production rate always leads to viral clearance, highlighting the promise of antibody therapies currently in clinical trials.
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21
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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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22
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Niklasch M, Zimmermann P, Nassal M. The Hepatitis B Virus Nucleocapsid-Dynamic Compartment for Infectious Virus Production and New Antiviral Target. Biomedicines 2021; 9:1577. [PMID: 34829806 PMCID: PMC8615760 DOI: 10.3390/biomedicines9111577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV's only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality.
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Affiliation(s)
| | | | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany; (M.N.); (P.Z.)
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23
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Genome chromatinization in giant double-stranded DNA viruses. Trends Biochem Sci 2021; 47:3-5. [PMID: 34657789 DOI: 10.1016/j.tibs.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/22/2022]
Abstract
Giant viruses have extravagantly large double-stranded (ds)DNA genomes that are packaged into exceedingly complex virions. In two recent papers, Liu et al. and Valencia-Sánchez, Abini-Agbomson et al. show that some giant viruses encode unique histone doublets, which form nucleosomes remarkably similar to those found across the eukaryotic domain of life.
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24
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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25
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Real-Hohn A, Blaas D. Rhinovirus Inhibitors: Including a New Target, the Viral RNA. Viruses 2021; 13:1784. [PMID: 34578365 PMCID: PMC8473194 DOI: 10.3390/v13091784] [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: 05/27/2021] [Revised: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Rhinoviruses (RVs) are the main cause of recurrent infections with rather mild symptoms characteristic of the common cold. Nevertheless, RVs give rise to enormous numbers of absences from work and school and may become life-threatening in particular settings. Vaccination is jeopardised by the large number of serotypes eliciting only poorly cross-neutralising antibodies. Conversely, antivirals developed over the years failed FDA approval because of a low efficacy and/or side effects. RV species A, B, and C are now included in the fifteen species of the genus Enteroviruses based upon the high similarity of their genome sequences. As a result of their comparably low pathogenicity, RVs have become a handy model for other, more dangerous members of this genus, e.g., poliovirus and enterovirus 71. We provide a short overview of viral proteins that are considered potential drug targets and their corresponding drug candidates. We briefly mention more recently identified cellular enzymes whose inhibition impacts on RVs and comment novel approaches to interfere with infection via aggregation, virus trapping, or preventing viral access to the cell receptor. Finally, we devote a large part of this article to adding the viral RNA genome to the list of potential drug targets by dwelling on its structure, folding, and the still debated way of its exit from the capsid. Finally, we discuss the recent finding that G-quadruplex stabilising compounds impact on RNA egress possibly via obfuscating the unravelling of stable secondary structural elements.
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Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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26
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Peabody DS, Peabody J, Bradfute SB, Chackerian B. RNA Phage VLP-Based Vaccine Platforms. Pharmaceuticals (Basel) 2021; 14:764. [PMID: 34451861 PMCID: PMC8401894 DOI: 10.3390/ph14080764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles from a variety of RNA bacteriophages have turned out to be useful platforms for delivery of vaccine antigens in a highly immunogenic format. Here we update the current state of development of RNA phage VLPs as platforms for presentation of diverse antigens by genetic, enzymatic, and chemical display methods.
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Affiliation(s)
- David S. Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
| | - Julianne Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
| | - Steven B. Bradfute
- Center for Global Health, Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 505, USA;
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (J.P.); (B.C.)
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27
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Brown RS, Kim L, Kielian M. Specific Recognition of a Stem-Loop RNA Structure by the Alphavirus Capsid Protein. Viruses 2021; 13:v13081517. [PMID: 34452382 PMCID: PMC8402798 DOI: 10.3390/v13081517] [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: 07/04/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/04/2023] Open
Abstract
Alphaviruses are small enveloped viruses with positive-sense RNA genomes. During infection, the alphavirus capsid protein (Cp) selectively packages and assembles with the viral genomic RNA to form the nucleocapsid core, a process critical to the production of infectious virus. Prior studies of the alphavirus Semliki Forest virus (SFV) showed that packaging and assembly are promoted by Cp binding to multiple high affinity sites on the genomic RNA. Here, we developed an in vitro Cp binding assay based on fluorescently labeled RNA oligos. We used this assay to explore the RNA sequence and structure requirements for Cp binding to site #1, the top binding site identified on the genomic RNA during all stages of virus assembly. Our results identify a stem-loop structure that promotes specific binding of the SFV Cp to site #1 RNA. This structure is also recognized by the Cps of the related alphaviruses chikungunya virus and Ross River virus.
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28
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Tetter S, Terasaka N, Steinauer A, Bingham RJ, Clark S, Scott AJP, Patel N, Leibundgut M, Wroblewski E, Ban N, Stockley PG, Twarock R, Hilvert D. Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein. Science 2021; 372:1220-1224. [PMID: 34112695 DOI: 10.1126/science.abg2822] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 12/14/2022]
Abstract
Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing nonviral carriers for diverse vaccine and delivery applications.
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Affiliation(s)
- Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Naohiro Terasaka
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Richard J Bingham
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Sam Clark
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Reidun Twarock
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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29
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Dechant PP, He YH. Machine-learning a virus assembly fitness landscape. PLoS One 2021; 16:e0250227. [PMID: 33951035 PMCID: PMC8099058 DOI: 10.1371/journal.pone.0250227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 04/01/2021] [Indexed: 02/05/2023] Open
Abstract
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.
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Affiliation(s)
- Pierre-Philippe Dechant
- School of Science, Technology & Health, York St John University, York, United Kingdom
- York Cross-disciplinary Centre for Systems Analysis, University of York, Heslington, United Kingdom
- Department of Mathematics, University of York, Heslington, United Kingdom
| | - Yang-Hui He
- Department of Mathematics, City, University of London, London, United Kingdom
- Merton College, University of Oxford, Oxford, United Kingdom
- School of Physics, NanKai University, Tianjin, P.R. China
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30
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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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31
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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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32
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Chandler-Bostock R, Mata CP, Bingham RJ, Dykeman EC, Meng B, Tuthill TJ, Rowlands DJ, Ranson NA, Twarock R, Stockley PG. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog 2020; 16:e1009146. [PMID: 33370422 PMCID: PMC7793301 DOI: 10.1371/journal.ppat.1009146] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/08/2021] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.
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Affiliation(s)
- Rebecca Chandler-Bostock
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Carlos P. Mata
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Richard J. Bingham
- 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
| | - Bo Meng
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Tobias J. Tuthill
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J. Rowlands
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - 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
- * E-mail: (DJR); (NAR); (RT); (PGS)
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (DJR); (NAR); (RT); (PGS)
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33
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San Emeterio J, Pollack L. Visualizing a viral genome with contrast variation small angle X-ray scattering. J Biol Chem 2020; 295:15923-15932. [PMID: 32913117 PMCID: PMC7681021 DOI: 10.1074/jbc.ra120.013961] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/04/2020] [Indexed: 01/14/2023] Open
Abstract
Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA.
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34
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Brown RS, Anastasakis DG, Hafner M, Kielian M. Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA. Nat Commun 2020; 11:4693. [PMID: 32943634 PMCID: PMC7499256 DOI: 10.1038/s41467-020-18447-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, here we comprehensively define binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrate Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments show that PS is not required for production of infectious SFV or Chikungunya virus. Instead, we identify multiple Cp binding sites that are enriched on gRNA-specific regions and promote infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrate that budding causes discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site is maintained throughout virus assembly, and specifically binds and assembles with Cp into core-like particles in vitro. Together our data suggest a model for selective alphavirus genome recognition and assembly. Alphaviruses need to selectively package genomic viral RNA for transmission, but the packaging mechanism remains unclear. Here, Brown et al. combine PAR-CLIP with biotinylated capsid protein (Cp) retrieval and identify multiple Cp binding sites on genomic viral RNA that promote virion formation.
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Affiliation(s)
- Rebecca S Brown
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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35
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Mata CP, Rodríguez JM, Suzuki N, Castón JR. Structure and assembly of double-stranded RNA mycoviruses. Adv Virus Res 2020; 108:213-247. [PMID: 33837717 DOI: 10.1016/bs.aivir.2020.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycoviruses are a diverse group that includes ssRNA, dsRNA, and ssDNA viruses, with or without a protein capsid, as well as with a complex envelope. Most mycoviruses are transmitted by cytoplasmic interchange and are thought to lack an extracellular phase in their infection cycle. Structural analysis has focused on dsRNA mycoviruses, which usually package their genome in a 120-subunit T=1 icosahedral capsid, with a capsid protein (CP) dimer as the asymmetric unit. The atomic structure is available for four dsRNA mycovirus from different families: Saccharomyces cerevisiae virus L-A (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). Their capsids show structural variations of the same framework, with asymmetric or symmetric CP dimers respectively for ScV-L-A and PsV-F, dimers of similar domains of a single CP for PcV, or of two different proteins for RnQV1. The CP dimer is the building block, and assembly proceeds through dimers of dimers or pentamers of dimers, in which the genome is packed as ssRNA by interaction with CP and/or viral polymerase. These capsids remain structurally undisturbed throughout the viral cycle. The T=1 capsid participates in RNA synthesis, organizing the viral polymerase (1-2 copies) and a single loosely packaged genome segment. It also acts as a molecular sieve, to allow the passage of viral transcripts and nucleotides, but to prevent triggering of host defense mechanisms. Due to the close mycovirus-host relationship, CP evolved to allocate peptide insertions with enzyme activity, as reflected in a rough outer capsid surface.
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Affiliation(s)
- Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Javier M Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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36
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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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37
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Valbuena A, Maity S, Mateu MG, Roos WH. Visualization of Single Molecules Building a Viral Capsid Protein Lattice through Stochastic Pathways. ACS NANO 2020; 14:8724-8734. [PMID: 32633498 PMCID: PMC7392527 DOI: 10.1021/acsnano.0c03207] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Direct visualization of pathways followed by single molecules while they spontaneously self-assemble into supramolecular biological machines may provide fundamental knowledge to guide molecular therapeutics and the bottom-up design of nanomaterials and nanodevices. Here, high-speed atomic force microscopy is used to visualize self-assembly of the bidimensional lattice of protein molecules that constitutes the framework of the mature human immunodeficiency virus capsid. By real-time imaging of the assembly reaction, individual transient intermediates and reaction pathways followed by single molecules could be revealed. As when assembling a jigsaw puzzle, the capsid protein lattice is randomly built. Lattice patches grow independently from separate nucleation events whereby individual molecules follow different paths. Protein subunits can be added individually, while others form oligomers before joining a lattice or are occasionally removed from the latter. Direct real-time imaging of supramolecular self-assembly has revealed a complex, chaotic process involving multiple routes followed by individual molecules that are inaccessible to bulk (averaging) techniques.
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Affiliation(s)
- Alejandro Valbuena
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Sourav Maity
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Mauricio G. Mateu
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
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38
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Luque D, Castón JR. Cryo-electron microscopy for the study of virus assembly. Nat Chem Biol 2020; 16:231-239. [PMID: 32080621 DOI: 10.1038/s41589-020-0477-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
Abstract
Although viruses are extremely diverse in shape and size, evolution has led to a limited number of viral classes or lineages, which is probably linked to the assembly constraints of a viable capsid. Viral assembly mechanisms are restricted to two general pathways, (i) co-assembly of capsid proteins and single-stranded nucleic acids and (ii) a sequential mechanism in which scaffolding-mediated capsid precursor assembly is followed by genome packaging. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), which are revolutionizing structural biology, are central to determining the high-resolution structures of many viral assemblies as well as those of assembly intermediates. This wealth of cryo-EM data has also led to the development and redesign of virus-based platforms for biomedical and biotechnological applications. In this Review, we will discuss recent viral assembly analyses by cryo-EM and cryo-ET showing how natural assembly mechanisms are used to encapsulate heterologous cargos including chemicals, enzymes, and/or nucleic acids for a variety of nanotechnological applications.
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Affiliation(s)
- Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, Madrid, Spain.
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39
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Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
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40
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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Twarock R, Luque A. Structural puzzles in virology solved with an overarching icosahedral design principle. Nat Commun 2019; 10:4414. [PMID: 31562316 PMCID: PMC6765026 DOI: 10.1038/s41467-019-12367-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022] Open
Abstract
Viruses have evolved protein containers with a wide spectrum of icosahedral architectures to protect their genetic material. The geometric constraints defining these container designs, and their implications for viral evolution, are open problems in virology. The principle of quasi-equivalence is currently used to predict virus architecture, but improved imaging techniques have revealed increasing numbers of viral outliers. We show that this theory is a special case of an overarching design principle for icosahedral, as well as octahedral, architectures that can be formulated in terms of the Archimedean lattices and their duals. These surface structures encompass different blueprints for capsids with the same number of structural proteins, as well as for capsid architectures formed from a combination of minor and major capsid proteins, and are recurrent within viral lineages. They also apply to other icosahedral structures in nature, and offer alternative designs for man-made materials and nanocontainers in bionanotechnology.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology, York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK.
| | - Antoni Luque
- Department of Mathematics and Statistics, Viral Information Institute, and Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-7720, USA.
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