160 results on '"Bromovirus"'
Search Results
2. Biomimetic Virus-Like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools
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Chan, Soo Khim, Du, Pinyi, Ignacio, Caroline, Mehta, Sanjay, Newton, Isabel G, and Steinmetz, Nicole F
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Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Horticultural Production ,Prevention ,Biodefense ,Pneumonia ,Biotechnology ,Emerging Infectious Diseases ,Pneumonia & Influenza ,Genetics ,Infectious Diseases ,Vaccine Related ,Lung ,Infection ,Bacteriophages ,Biomimetics ,Bromovirus ,COVID-19 ,COVID-19 Testing ,Humans ,Kinetics ,Nanotechnology ,RNA ,Viral ,Reproducibility of Results ,Reverse Transcriptase Polymerase Chain Reaction ,SARS-CoV-2 ,Vaccines ,Virus-Like Particle ,virus-like particles ,reverse transcription polymerase chain reaction ,phage Q beta ,cowpea chlorotic mottle virus ,COVID-19 ,SARS-CoV-2 ,phage Qβ ,Nanoscience & Nanotechnology - Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible disease that has affected more than 90% of the countries worldwide. At least 17 million individuals have been infected, and some countries are still battling first or second waves of the pandemic. Nucleic acid tests, especially reverse transcription polymerase chain reaction (RT-PCR), have become the workhorse for early detection of COVID-19 infection. Positive controls for the molecular assays have been developed to validate each test and to provide high accuracy. However, most available positive controls require cold-chain distribution and cannot serve as full-process control. To overcome these shortcomings, we report the production of biomimetic virus-like particles (VLPs) as SARS-CoV-2 positive controls. A SARS-CoV-2 detection module for RT-PCR was encapsidated into VLPs from a bacteriophage and a plant virus. The chimeric VLPs were obtained either by in vivo reconstitution and coexpression of the target detection module and coat proteins or by in vitro assembly of purified detection module RNA sequences and coat proteins. These VLP-based positive controls mimic SARS-CoV-2 packaged ribonucleic acid (RNA) while being noninfectious. Most importantly, we demonstrated that the positive controls are scalable, stable, and can serve broadly as controls, from RNA extraction to PCR in clinical settings.
- Published
- 2021
3. Genome organization and interaction with capsid protein in a multipartite RNA virus
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Beren, Christian, Cui, Yanxiang, Chakravarty, Antara, Yang, Xue, Rao, ALN, Knobler, Charles M, Zhou, Z Hong, and Gelbart, William M
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Infection ,Bacteriophages ,Bromovirus ,Capsid Proteins ,Genome ,Viral ,RNA ,Viral ,cryoelectron microscopy ,virus ,single-stranded RNA - Abstract
We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes.
- Published
- 2020
4. Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo.
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Chakravarty, Antara, Reddy, Vijay, and Rao, A
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MALDI-TOF ,RNA virus ,capsid dynamics ,genome packaging ,stability ,Agrobacterium ,Bromovirus ,Capsid ,Capsid Proteins ,Genome ,Viral ,Peptide Mapping ,RNA ,Bacterial ,RNA ,Viral ,Virion ,Virus Assembly ,Virus Replication - Abstract
Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1V) and type 2 (B2V) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4V) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K65, R103, K111, and K165 on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1V and B2V released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4V capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
- Published
- 2020
5. Delivery of siRNA therapeutics using cowpea chlorotic mottle virus-like particles
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Lam, Patricia and Steinmetz, Nicole F
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Genetics ,Biotechnology ,Gene Therapy ,Bromovirus ,Cell-Penetrating Peptides ,Drug Carriers ,Gene Silencing ,Genetic Therapy ,HeLa Cells ,Hepatocyte Nuclear Factor 3-alpha ,Humans ,MCF-7 Cells ,RNA ,Small Interfering ,Hela Cells ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Medical Biotechnology - Abstract
While highly promising in medicine, gene therapy requires delivery agents to protect and target nucleic acid therapeutics. We developed a plant viral siRNA delivery platform making use of self-assembling cowpea chlorotic mottle virus (CCMV). CCMV was loaded with siRNAs targeting GFP or FOXA1; to further enhance cell uptake and intracellular trafficking, resulting in more efficient gene knockdown, we appended CCMV with a cell penetrating peptide (CPP), specifically M-lycotoxin peptide L17E.
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- 2019
6. Viruses Infecting Bulbous Ornamental Plants and Their Diagnosis and Management
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Madhavan, S., Balasubramanian, V., Selvarajan, R., Raj, S. K., editor, Gaur, Rajarshi Kumar, editor, and Yin, Zhimin, editor
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- 2021
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7. The Effect of RNA Secondary Structure on the Self-Assembly of Viral Capsids
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Beren, Christian, Dreesens, Lisa L, Liu, Katherine N, Knobler, Charles M, and Gelbart, William M
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Biological Sciences ,Bioinformatics and Computational Biology ,Bromovirus ,Capsid ,Capsid Proteins ,Electrophoretic Mobility Shift Assay ,Microscopy ,Electron ,Transmission ,Nucleic Acid Conformation ,RNA ,Viral ,Virus Assembly ,Physical Sciences ,Chemical Sciences ,Biophysics ,Biological sciences ,Chemical sciences ,Physical sciences - Abstract
Previous work has shown that purified capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) is capable of packaging both purified single-stranded RNA molecules of normal composition (comparable numbers of A, U, G, and C nucleobases) and of varying length and sequence, and anionic synthetic polymers such as polystyrene sulfonate. We find that CCMV CP is also capable of packaging polyU RNAs, which-unlike normal-composition RNAs-do not form secondary structures and which act as essentially structureless linear polymers. Following our canonical two-step assembly protocol, polyU RNAs ranging in length from 1000 to 9000 nucleotides (nt) are completely packaged. Surprisingly, negative-stain electron microscopy shows that all lengths of polyU are packaged into 22-nm-diameter particles despite the fact that CCMV CP prefers to form 28-nm-diameter (T = 3) particles when packaging normal-composition RNAs. PolyU RNAs >5000 nt in length are packaged into multiplet capsids, in which a single RNA molecule is shared between two or more 22-nm-diameter capsids, in analogy with the multiplets of 28-nm-diameter particles formed with normal-composition RNAs >5000 nt long. Experiments in which viral RNA competes for viral CP with polyUs of equal length show that polyU, despite its lack of secondary structure, is packaged more efficiently than viral RNA. These findings illustrate that the secondary structure of the RNA molecule-and its absence-plays an essential role in determining capsid structure during the self-assembly of CCMV-like particles.
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- 2017
8. Viral diseases of legumes in the south of the Russian Far East
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N. N. Kakareka, Yu. G. Volkov, V. F. Tolkach, T. V. Tabakaeva, Yu. A. Belov, A. A. Muratov, and M. Yu. Shchelkanov
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бобовые ,fabaceae ,фитовирусы ,alfamovirus ,bromovirus ,cucumovirus ,unidentified ,potyvirus ,nepovirus ,enamovirus ,potexvirus ,carlavirus ,Ecology ,QH540-549.5 - Abstract
Aim. The aim of the current work is to analyse the epiphytotic situation in the south of the Russian Far East in connection with viral diseases of legumes (Fabaceae Lindl., 1836).Discussion contains a description of 18 viruses that infect legumes in this region: Alfalfa mosaic (Martellivirales: Bromoviridae, Alfamovirus); Vicia unijuga mosaic (Martellivirales: Bromoviridae, Bromovirus); Cucumber mosaic (Martellivirales: Bromoviridae, Cucumovirus); Vicia unijuga ringspot virus (Martellivirales: Closteroviridae, Unidentified); Trifolium hybridum yellow mosaic virus, Bean common mosaic virus, Bean yellow mosaic virus, Trifolium repens mottle virus, Mountain clover mosaic virus, Red clover mosaic virus, Soybean chlorotic deformation virus, Soybean chlorotic mottle virus, Soybean mosaic virus, Soybean weak mosaic virus (Patatavirales: Genus, Potyvirus); Tobacco ringspot virus (Picornavirales: Secoviridae, Nepovirus); Pea enation mosaic virus (Tolivirales: Luteoviridae, Enamovirus); White clover mosaic virus (Tymovirales: Alphaflexiviridae, Potexvirus); Vicia pseudorobus necrotic mosaic virus (Tymovirales: Betaflexiviridae, Carlavirus). The description of the established natural reservoirs and the main vectors of these viruses is given.Conclusion. A list of measures are recommended for the prevention of viral diseases of legumes and a thesis is provided on the need to continue the planned monitoring of the phytovirological situation in the Russian Far East.
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- 2022
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9. Ultrafast Collective Excited-State Dynamics of a Virus-Supported Fluorophore Antenna
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Joseph Holmes, Arathi Anil Sushma, Irina B. Tsvetkova, William L. Schaich, Richard D. Schaller, and Bogdan Dragnea
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Spectrometry, Fluorescence ,Viruses ,General Materials Science ,Physical and Theoretical Chemistry ,Bromovirus ,Article ,Fluorescent Dyes - Abstract
Radiation brightening was recently observed in a multifluorophore-conjugated brome mosaic virus (BMV) particle at room temperature under pulsed excitation. On the basis of its nonlinear dependence on the number of chromophores, the origins of the phenomenon were attributed to a collective relaxation. However, the mechanism remains unknown. We present ultrafast transient absorption and fluorescence spectroscopic studies which shed new light on the collective nature of the relaxation dynamics in such radiation-brightened, multifluorophore particles. Our findings indicate that the emission dynamics is consistent with a superradiance mechanism. The ratio between the rates of competing radiative and nonradiative relaxation pathways depends on the number of chromophores per virus. The findings suggest that small icosahedral virus shells provide a unique biological scaffold for developing nonclassical, deep subwavelength light sources and may open new avenues for the development of photonic probes for medical imaging applications.
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- 2022
10. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure
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Madeline E. Sherlock, Jeffrey S. Kieft, Steve Bonilla, and Andrea MacFadden
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Models, Molecular ,Phaseolus ,Multidisciplinary ,Protein Conformation ,Host (biology) ,Extramural ,viruses ,Cryoelectron Microscopy ,Molecular Mimicry ,food and beverages ,RNA ,Genome, Viral ,Computational biology ,Biology ,Virus Replication ,Bromovirus ,Article ,RNA, Transfer ,Tyrosine-tRNA Ligase ,Transfer RNA ,Nucleic Acid Conformation ,RNA, Viral ,Viral rna ,Transfer RNA Aminoacylation ,Protein Binding - Abstract
Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.
- Published
- 2021
11. An Evolved 5' Untranslated Region of Alfalfa Mosaic Virus Allows the RNA Transport of Movement-Defective Variants
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David Villar-Álvarez, Vicente Pallás, Santiago F. Elena, and Jesús A. Sánchez-Navarro
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Plant Viral Movement Proteins ,AMV model system ,BMV ,cell-to-cell and systemic movement ,virus particles ,Virology ,Insect Science ,Alfalfa mosaic virus ,Immunology ,RNA, Viral ,5' Untranslated Regions ,Microbiology ,Bromovirus ,RNA Transport - Abstract
Although the coat protein (CP) has a relevant role in the long-distance movement of alfalfa mosaic virus (AMV) and brome mosaic virus (BMV), its precise function is not fully understood. Previous results showed that a specific interaction between the C termini of the movement protein (MP) and the cognate CP is required for systemic transport. Thus, we have performed a compensatory evolution experiment using an AMV RNA3 derivative defective in long-distance transport that carries a BMV MP lacking the C-terminal 48 residues and unable to interact with the AMV CP. After several passages, five independent evolution lineages were able to move long distance. The analysis of the viral RNA of these lineages showed the presence of three different modifications located exclusively at the 5' untranslated region (5' UTR). The three evolved 5' UTR variants accumulated comparable levels of viral RNA and CP but reduced the accumulation of virus particles and the affinity between the 5' UTR and the AMV CP. In addition, the evolved 5' UTR increased cell-to-cell transport for both the AMV RNA3 carrying the BMV MP and that carrying the AMV MP. Finally, the evolved 5' UTRs allowed the systemic transport of an AMV RNA3 carrying a CP mutant defective in virus particles and increased the systemic transport of several AMV RNA3 derivatives carrying different viral MPs associated with the 30K superfamily. Altogether, our findings indicate that virus particles are not required for the systemic transport of AMV but also that BMV MP is competent for the short- and long-distance transport without the interaction with the CP. IMPORTANCE The results obtained in the present work could challenge the view of the role of the virus particle in the systemic transport of plant viruses. In this sense, we show that two different MPs are competent to systemically transport the AMV genome without the requirement of the virus particles, as reported for viruses lacking a CP (e.g., Umbravirus). The incapability of the viral MP to interact with the CP triggered virus variants that evolved to reduce the formation of virus particles, probably to increase the accessibility of the MP to the viral progeny. Our results point to the idea that virus particles would not be necessary for the viral systemic transport but would be necessary for vector virus transmission. This idea is reinforced by the observation that heterologous MPs also increased the systemic transport of the AMV constructs that have reduced encapsidation capabilities.
- Published
- 2022
12. TLR Agonists Delivered by Plant Virus and Bacteriophage Nanoparticles for Cancer Immunotherapy.
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Jung E, Chung YH, and Steinmetz NF
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- Animals, Mice, Toll-Like Receptor 3, Toll-Like Receptor 7, Adjuvants, Immunologic, Immunotherapy, Plant Viruses, Bromovirus, Bacteriophages, Neoplasms drug therapy
- Abstract
Toll-like receptors (TLRs) are promising targets in cancer immunotherapy due to their role in activating the immune system; therefore, various small-molecule TLR agonists have been tested in clinical applications. However, the clinical use of TLR agonists is hindered by their non-specific side effects and poor pharmacokinetics. To overcome these limitations, we used plant virus nanoparticles (VNPs) and bacteriophage virus-like particles (VLPs) as drug delivery systems. We conjugated TLR3 or TLR7 agonists to cowpea mosaic virus (CPMV) VNPs, cowpea chlorotic mottle virus (CCMV) VNPs, and bacteriophage Qβ VLPs. The conjugation of TLR7 agonist, 2-methoxyethoxy-8-oxo-9-(4-carboxybenzyl)adenine (1V209), resulted in the potent activation of immune cells and promoted the production of pro-inflammatory cytokine interleukin 6. We found that 1V209 conjugated to CPMV, CCMV, and Qβ reduced tumor growth in vivo and prolonged the survival of mice compared to those treated with free 1V209 or a simple admixture of 1V209 and viral particles. Nucleic acid-based TLR3 agonist, polyinosinic acid with polycytidylic acid (poly(I:C)), was also delivered by CPMV VNPs, resulting in enhanced mice survival. All our data suggest that coupling and co-delivery are required to enhance the anti-tumor efficacy of TLR agonists and simple mixing of the VLPs with the agonists does not confer a survival benefit. The delivery of 1V209 or poly(I:C) conjugated to VNPs/VLPs probably enhances their efficacy due to the multivalent presentation, prolongation of tumor residence time, and targeting of the innate immune cells mediated by the VNP/VLP carrier.
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- 2023
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13. Fast viral dynamics revealed by microsecond time-resolved cryo-EM.
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Harder OF, Barrass SV, Drabbels M, and Lorenz UJ
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- Cryoelectron Microscopy, Capsid, Capsid Proteins, Motion, Bromovirus
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Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function., (© 2023. Springer Nature Limited.)
- Published
- 2023
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14. Relaxational dynamics of the T-number conversion of virus capsids.
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Clark AB, Safdari M, Zoorob S, Zandi R, and van der Schoot P
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- Capsid Proteins, Kinetics, Virion, Capsid, Bromovirus
- Abstract
We extend a recently proposed kinetic theory of virus capsid assembly based on Model A kinetics and study the dynamics of the interconversion of virus capsids of different sizes triggered by a quench, that is, by sudden changes in the solution conditions. The work is inspired by in vitro experiments on functionalized coat proteins of the plant virus cowpea chlorotic mottle virus, which undergo a reversible transition between two different shell sizes (T = 1 and T = 3) upon changing the acidity and salinity of the solution. We find that the relaxation dynamics are governed by two time scales that, in almost all cases, can be identified as two distinct processes. Initially, the monomers and one of the two types of capsids respond to the quench. Subsequently, the monomer concentration remains essentially constant, and the conversion between the two capsid species completes. In the intermediate stages, a long-lived metastable steady state may present itself, where the thermodynamically less stable species predominate. We conclude that a Model A based relaxational model can reasonably describe the early and intermediate stages of the conversion experiments. However, it fails to provide a good representation of the time evolution of the state of assembly of the coat proteins in the very late stages of equilibration when one of the two species disappears from the solution. It appears that explicitly incorporating the nucleation barriers to assembly and disassembly is crucial for an accurate description of the experimental findings, at least under conditions where these barriers are sufficiently large., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)
- Published
- 2023
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15. Ecological Strategies for Resource Use by Three Bromoviruses in Anthropic and Wild Plant Communities.
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Babalola B, Fraile A, García-Arenal F, and McLeish M
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- Genetic Drift, High-Throughput Nucleotide Sequencing, Host Specificity, Ecosystem, Bromovirus
- Abstract
Ecological strategies for resource utilisation are important features of pathogens, yet have been overshadowed by stronger interest in genetic mechanisms underlying disease emergence. The purpose of this study is to ask whether host range and transmission traits translate into ecological strategies for host-species utilisation in a heterogeneous ecosystem, and whether host utilisation corresponds to genetic differentiation among three bromoviruses. We combine high-throughput sequencing and population genomics with analyses of species co-occurrence to unravel the ecological strategies of the viruses across four habitat types. The results show that the bromoviruses that were more closely related genetically did not share similar ecological strategies, but that the more distantly related pair did. Shared strategies included a broad host range and more frequent co-occurrences, which both were habitat-dependent. Each habitat thus presents as a barrier to gene flow, and each virus has an ecological strategy to navigate limitations to colonising non-natal habitats. Variation in ecological strategies could therefore hold the key to unlocking events that lead to emergence., Competing Interests: The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.
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- 2023
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16. Single-particle studies of the effects of RNA–protein interactions on the self-assembly of RNA virus particles
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Rees F. Garmann, Aaron M. Goldfain, Cheylene R. Tanimoto, Christian E. Beren, Fernando F. Vasquez, Daniel A. Villarreal, Charles M. Knobler, William M. Gelbart, and Vinothan N. Manoharan
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Capsid ,Multidisciplinary ,Virion ,RNA Viruses ,RNA, Viral ,Bromovirus - Abstract
Understanding the pathways by which simple RNA viruses self-assemble from their coat proteins and RNA is of practical and fundamental interest. Although RNA–protein interactions are thought to play a critical role in the assembly, our understanding of their effects is limited because the assembly process is difficult to observe directly. We address this problem by using interferometric scattering microscopy, a sensitive optical technique with high dynamic range, to follow the in vitro assembly kinetics of more than 500 individual particles of brome mosaic virus (BMV)—for which RNA–protein interactions can be controlled by varying the ionic strength of the buffer. We find that when RNA–protein interactions are weak, BMV assembles by a nucleation-and-growth pathway in which a small cluster of RNA-bound proteins must exceed a critical size before additional proteins can bind. As the strength of RNA–protein interactions increases, the nucleation time becomes shorter and more narrowly distributed, but the time to grow a capsid after nucleation is largely unaffected. These results suggest that the nucleation rate is controlled by RNA–protein interactions, while the growth process is driven less by RNA–protein interactions and more by protein–protein interactions and intraprotein forces. The nucleated pathway observed with the plant virus BMV is strikingly similar to that previously observed with bacteriophage MS2, a phylogenetically distinct virus with a different host kingdom. These results raise the possibility that nucleated assembly pathways might be common to other RNA viruses.
- Published
- 2022
17. Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers
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Janos Szoverfi and Szilard N. Fejer
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Capsid ,Multidisciplinary ,Capsid Proteins ,Molecular Dynamics Simulation ,Sodium Chloride ,Bromovirus - Abstract
Intermediates of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales either by studying oligomers in equilibrium or by focusing on their dissociation instead of their association. Our previous studies showed that among the three possible dimer interfaces in the icosahedral capsid, two are thermodynamically relevant for capsid formation. The aim of the current study is to evaluate the relative structural stabilities of the three different ss-CCMV dimers and to find and understand the conditions that lead to their dissociation. Long timescale molecular dynamics simulations at 300 K of the various dimers and of the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. Simulations in implicit solvent show that at higher temperature (350 K), the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable interface. The pentamer of dimers is also found to be stable on long timescales at 300 K, with an inherent flexibility of the outer protein chains.
- Published
- 2022
18. The dynamics of viruslike capsid assembly and disassembly
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Suzanne B. P. E. Timmermans, Alireza Ramezani, Toni Montalvo, Mark Nguyen, Paul van der Schoot, Jan C. M. van Hest, Roya Zandi, Group Luttge, ICMS Core, Soft Matter and Biological Physics, Institute for Complex Molecular Systems, and Bio-Organic Chemistry
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Capsid ,Colloid and Surface Chemistry ,Biological Physics (physics.bio-ph) ,Virus Assembly ,Virion ,RNA, Viral ,FOS: Physical sciences ,Capsid Proteins ,General Chemistry ,Physics - Biological Physics ,Bromovirus ,Biochemistry ,Catalysis - Abstract
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral RNA in assembly and disassembly processes. Here, we report on the spontaneous and reversible size conversion of the empty capsids of a CCMV capsid protein functionalized with a hydrophobic elastin-like polypeptide which occurs following a pH jump. We monitor the concentrations of T = 3 and T = 1 capsids as a function of time and show that the time evolution of the conversion from one T number to another is not symmetric: The conversion from T = 1 to T = 3 is a factor of 10 slower than that of T = 3 to T = 1. We explain our experimental findings using a simple model based on classical nucleation theory applied to virus capsids, in which we account for the change in the free protein concentration, as the different types of shells assemble and disassemble by shedding or absorbing single protein subunits. As far as we are aware, this is the first study confirming that both the assembly and disassembly of viruslike shells can be explained through classical nucleation theory, reproducing quantitatively results from time-resolved experiments.
- Published
- 2022
19. Duplex-RT-PCR assay for the simultaneous detection and discrimination of Brome mosaic virus and Cocksfoot mottle virus in cereal plants
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Katarzyna Trzmiel
- Subjects
0106 biological sciences ,0301 basic medicine ,Crops, Agricultural ,Cocksfoot mottle virus ,CfMV ,viruses ,Short Communication ,RNA-dependent RNA polymerase ,Poaceae ,01 natural sciences ,Rapid detection ,Plant Viruses ,03 medical and health sciences ,Viral Proteins ,Brome mosaic virus ,Genetics ,Cereal plants ,Molecular Biology ,Gene ,Diagnostics ,Phytosanitary certification ,Plant Diseases ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,BMV ,food and beverages ,Hordeum ,General Medicine ,biology.organism_classification ,Virology ,Bromovirus ,Co-infection ,030104 developmental biology ,Real-time polymerase chain reaction ,Duplex (building) ,Duplex-RT-PCR ,RNA, Viral ,Edible Grain ,010606 plant biology & botany - Abstract
Brome mosaic virus (BMV) and cocksfoot mottle virus (CfMV) are pathogens of grass species including all economically important cereals. Both viruses have been identified in Poland therefore they create a potential risk to cereal crops. In this study, a duplex—reverse transcription—polymerase chain reaction (duplex-RT-PCR) was developed and optimized for simultaneous detection and differentiation of BMV and CfMV as well as for confirmation of their co-infection. Selected primers CfMVdiag-F/CfMVdiag-R and BMV2-F/BMV2-R amplified 390 bp and 798 bp RT-PCR products within coat protein (CP) region of CfMV and replicase gene of BMV, respectively. Duplex-RT-PCR was successfully applied for the detection of CfMV-P1 and different Polish BMV isolates. Moreover, one sample was found to be co-infected with BMV-ML1 and CfMV-ML1 isolates. The specificity of generated RT-PCR products was verified by sequencing. Duplex-RT-PCR, like conventional RT-PCR, was able to detect two viruses occurring in plant tissues in very low concentration (as low as 4.5 pg/µL of total RNA). In contrast to existing methods, newly developed technique offers a significant time and cost-saving advantage. In conclusion, duplex-RT-PCR is a useful tool which can be implemented by phytosanitary services to rapid detection and differentiation of BMV and CfMV.
- Published
- 2021
20. Dual Site-Selective Presentation of Functional Handles on Protein-Engineered Cowpea Chlorotic Mottle Virus-Like Particles
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Marleen H. M. E. van Stevendaal, Jan C. M. van Hest, Robin Heiringhoff, Suzanne B. P. E. Timmermans, Daan F. M. Vervoort, Institute for Complex Molecular Systems, Bio-Organic Chemistry, ICMS Core, and ICMS Business Operations
- Subjects
viruses ,Biomedical Engineering ,Pharmaceutical Science ,Bioengineering ,02 engineering and technology ,Protein Engineering ,01 natural sciences ,Article ,Residue (chemistry) ,Capsid ,Humans ,Pharmacology ,chemistry.chemical_classification ,Cowpea chlorotic mottle virus ,biology ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Protein engineering ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Bromovirus ,0104 chemical sciences ,Amino acid ,Drug delivery ,Biophysics ,PEGylation ,0210 nano-technology ,HeLa Cells ,Biotechnology ,Cysteine - Abstract
Protein cages hold much promise as carrier systems in nanomedicine, due to their well-defined size, cargo-loading capacity, and inherent biodegradability. In order to make them suitable for drug delivery, they have to be stable under physiological conditions. In addition, often surface modifications are required, for example, to improve cell targeting or reduce the particle immunogenicity by PEGylation. For this purpose, we investigated the functionalization capacity of the capsid of cowpea chlorotic mottle virus (CCMV), modified at the interior with a stabilizing elastin-like polypeptide (ELP) tag, by employing a combination of protein engineering and bio-orthogonal chemistry. We first demonstrated the accessibility of the native cysteine residue in ELP-CCMV as a site-selective surface-exposed functional handle, which was not available in the native CCMV capsid. An additional bio-orthogonal functional handle was introduced by incorporation of the noncanonical amino acid, azido-phenylalanine (AzF), using the amber suppression mechanism. Dual site-selective presentation of both a cell-penetrating TAT peptide and a fluorophore to track the particles was demonstrated successfully in HeLa cell uptake studies.
- Published
- 2021
21. Production and characterization of chimeric SARS-CoV-2 antigens based on the capsid protein of cowpea chlorotic mottle virus
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Claudia Almendárez-Rodriguez, Karla I. Solis-Andrade, Dania O. Govea-Alonso, Mauricio Comas-Garcia, and Sergio Rosales-Mendoza
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Chimera ,SARS-CoV-2 ,COVID-19 ,General Medicine ,Biochemistry ,Bromovirus ,Epitopes ,Mice ,Structural Biology ,Spike Glycoprotein, Coronavirus ,Vaccines, Subunit ,Escherichia coli ,Animals ,Humans ,Capsid Proteins ,Molecular Biology ,Pandemics - Abstract
The COVID-19 pandemic has highlighted the need for new vaccine platforms to rapidly develop solutions against emerging pathogens. In particular, some plant viruses offer several advantages for developing subunit vaccines, such as high expression rates in E. coli, high immunogenicity and safety, and absence of pre-immunity that could interfere with the vaccine's efficacy. Cowpea chlorotic mottle virus (CCMV) is a model system that has been extensively characterized, with key advantages for its use as an epitope carrier. In the present study, three relevant epitopes from the SARS-CoV-2 Spike protein were genetically inserted into the CCMV CP and expressed in E. coli cultures, resulting in the CCMV1, CCMV2, and CCMV3 chimeras. The recombinant CP mutants were purified from the formed inclusion bodies and refolded, and their immunogenicity as a subunit vaccine was assessed in BALB/c mice. The three mutants are immunogenic as they induce high IgG antibody titers that recognize the recombinant full-length S protein. This study supports the application of CCMV CP as an attractive carrier for the clinical evaluation of vaccine candidates against SARS-CoV-2. Furthermore, it suggests that VLPs assembled from these chimeric proteins could result in antigens with better immunogenicity.
- Published
- 2022
22. Virus-Induced Gene Silencing in Sorghum Using Brome Mosaic Virus
- Author
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Dharmendra K, Singh and Kirankumar S, Mysore
- Subjects
Humans ,Gene Silencing ,Edible Grain ,Bromovirus ,Software ,Sorghum - Abstract
Sorghum [Sorghum bicolor (L.) Moench.] is a versatile crop, grown in 30 countries and a food source for nearly 500 million people globally. Although the sorghum genome is sequenced, a limited understanding of gene function prevents the improvement of resistance against almost 150 species of viruses, bacteria, fungus, and parasitic plants to improve productivity. Here, we present a Brome mosaic virus (BMV)-based virus-induced gene silencing (VIGS) to silence target genes for functional study in sorghum. This protocol achieves 100% sorghum infection with BMV by growing the plants at 18 °C instead of 22 °C. Using this method, one can achieve gene silencing in sorghum up to 100% of the inoculated plants.
- Published
- 2022
23. Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure
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Milosz Ruszkowski, Aleksander Strugala, Paulina Indyka, Guillaume Tresset, Marek Figlerowicz, and Anna Urbanowicz
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Capsid ,viruses ,Virus Assembly ,Cryoelectron Microscopy ,Virion ,virus diseases ,General Materials Science ,Capsid Proteins ,biochemical phenomena, metabolism, and nutrition ,complex mixtures ,Bromovirus - Abstract
The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features
- Published
- 2022
24. Disassembly Intermediates of the Brome Mosaic Virus Identified by Charge Detection Mass Spectrometry
- Author
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Nicholas A. Lyktey, Irina B. Tsvetkova, Kevin M. Bond, Bogdan Dragnea, and Martin F. Jarrold
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viruses ,010402 general chemistry ,Cleavage (embryo) ,01 natural sciences ,Mass Spectrometry ,Virus ,Divalent ,Capsid ,Brome mosaic virus ,0103 physical sciences ,Materials Chemistry ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,010304 chemical physics ,biology ,Chemistry ,Virion ,RNA ,Translation (biology) ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Bromovirus ,In vitro ,0104 chemical sciences ,Surfaces, Coatings and Films ,Biophysics ,RNA, Viral ,Capsid Proteins - Abstract
Capsid disassembly and genome release are critical steps in the lifecycle of a virus. However, their mechanisms are poorly understood, both in vivo and in vitro. Here, we have identified two in vitro disassembly pathways of the brome mosaic virus (BMV) by charge detection mass spectrometry and transmission electron microscopy. When subjected to a pH jump to a basic environment at low ionic strength, protein-RNA interactions are disrupted. Under these conditions, BMV appears to disassemble mainly through a global cleavage event into two main fragments: a near complete capsid that has released the RNA and the released RNA complexed to a small number of the capsid proteins. Upon slow buffer exchange to remove divalent cations at neutral pH, capsid protein interactions are disrupted. The BMV virions swell but there is no measurable loss of the RNA. Some of the virions break into small fragments, leading to an increase in the abundance of species with masses less than 1 MDa. The peak attributed to the BMV virion shifts to a higher mass with time. The mass increase is attributed to additional capsid proteins associating with the disrupted capsid protein-RNA complex, where the RNA is presumably partially exposed. It is likely that this pathway is more closely related to how the capsid disassembles in vivo, as it offers the advantage of protecting the RNA with the capsid protein until translation begins.
- Published
- 2020
25. Elucidating the Thermodynamic Driving Forces of Polyanion-Templated Virus-like Particle Assembly
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Jurriaan Huskens, Jeroen J. L. M. Cornelissen, Stan J. Maassen, Biomolecular Nanotechnology, and Molecular Nanofabrication
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Polymers ,viruses ,Static Electricity ,UT-Hybrid-D ,DNA, Single-Stranded ,010402 general chemistry ,01 natural sciences ,Article ,Hydrophobic effect ,Polystyrene sulfonate ,chemistry.chemical_compound ,Virus-like particle ,0103 physical sciences ,Materials Chemistry ,Physical and Theoretical Chemistry ,Cowpea chlorotic mottle virus ,010304 chemical physics ,biology ,Virus Assembly ,Temperature ,Isothermal titration calorimetry ,Hydrogen-Ion Concentration ,biology.organism_classification ,Bromovirus ,Polyelectrolytes ,0104 chemical sciences ,Surfaces, Coatings and Films ,Capsid ,chemistry ,Biophysics ,Polystyrenes ,Thermodynamics ,Particle ,Capsid Proteins ,DNA - Abstract
A virus in its most simple form is comprised of a protein capsid that surrounds and protects the viral genome. The self-assembly of such structures, however, is a highly complex, multiprotein, multiinteraction process and has been a topic of study for a number of years. This self-assembly process is driven by the (mainly electrostatic) interaction between the capsid proteins (CPs) and the genome as well as by the protein–protein interactions, which primarily rely on hydrophobic interactions. Insight in the thermodynamics that is involved in virus and virus-like particle (VLP) formation is crucial in the detailed understanding of this complex assembly process. Therefore, we studied the assembly of CPs of the cowpea chlorotic mottle virus (CCMV) templated by polyanionic species (cargo), that is, single-stranded DNA (ssDNA), and polystyrene sulfonate (PSS) using isothermal titration calorimetry. By separating the electrostatic CP–cargo interaction from the full assembly interaction, we conclude that CP–CP interactions cause an enthalpy change of −3 to −4 kcal mol–1 CP. Furthermore, we quantify that upon reducing the CP–CP interaction, in the case of CCMV by increasing the pH to 7, the CP–cargo starts to dominate VLP formation. This is highlighted by the three times higher affinity between CP and PSS compared to CP and ssDNA, resulting in the disassembly of CCMV at neutral pH in the presence of PSS to yield PSS-filled VLPs.
- Published
- 2019
26. Hydrophobic Cargo Encapsulation into Virus Protein Cages by Self-Assembly in an Aprotic Organic Solvent
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Xingchen Ye, Irina B. Tsvetkova, Yang Liu, Amberly Xie, Bogdan Dragnea, Ruben D Cadena-Nava, and Priyadarshine Hewavitharanage
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Pharmacology ,Aqueous solution ,biology ,Chemistry ,Dimethyl sulfoxide ,viruses ,Organic Chemistry ,Biomedical Engineering ,Pharmaceutical Science ,Nanoparticle ,Bioengineering ,biology.organism_classification ,Combinatorial chemistry ,Bromovirus ,Solvent ,chemistry.chemical_compound ,Brome mosaic virus ,Capsid ,Self-assembly ,BODIPY ,Biotechnology - Abstract
While extensive studies of virus capsid assembly in environments mimicking in vivo conditions have led to an understanding of the thermodynamic driving forces at work, applying this knowledge to virus assembly in other solvents than aqueous buffers has not been attempted yet. In this study, Brome mosaic virus (BMV) capsid proteins were shown to preserve their self-assembly abilities in an aprotic polar solvent, dimethyl sulfoxide (DMSO). This facilitated protein cage encapsulation of nanoparticles and dye molecules that favor organic solvents, such as β-NaYF4-based upconversion nanoparticles and BODIPY dye. Assembly was found to be robust relative to a surprisingly broad range of DMSO concentrations. Cargos with poor initial stability in aqueous solutions were readily encapsulated at high DMSO concentrations and then transferred to aqueous solvents, where they remained stable and preserved their function for months.
- Published
- 2021
27. Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles
- Author
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Bingqing Zhao, Irina B. Tsvetkova, Carolina Pérez-Segura, Jodi A. Hadden-Perilla, Bogdan Dragnea, James P. Reilly, and Arathi Anil Sushma
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Fluorophore ,biology ,Chemistry ,Icosahedral symmetry ,Coat protein ,Radiation ,biology.organism_classification ,Bromovirus ,Article ,Surfaces, Coatings and Films ,Molecular dynamics ,chemistry.chemical_compound ,Capsid ,Brome mosaic virus ,Viruses ,Materials Chemistry ,Biophysics ,Concentration quenching ,Capsid Proteins ,Physical and Theoretical Chemistry ,Fluorescent Dyes - Abstract
In certain conditions, dye-conjugated icosahedral virus shells exhibit suppression of concentration quenching. The recently observed radiation brightening at high fluorophore densities has been attributed to coherent emission, i.e., to a cooperative process occurring within a subset of the virus-supported fluorophores. Until now, the distribution of fluorophores among potential conjugation sites and the nature of the active subset remained unknown. With the help of mass spectrometry and molecular dynamics simulations, we found which conjugation sites in the brome mosaic virus capsid are accessible to fluorophores. Reactive external surface lysines but also those at the lumenal interface where the coat protein N-termini are located showed virtually unrestricted access to dyes. The third type of labeled lysines was situated at the intercapsomeric interfaces. Through limited proteolysis of flexible N-termini, it was determined that dyes bound to them are unlikely to be involved in the radiation brightening effect. At the same time, specific labeling of genetically inserted cysteines on the exterior capsid surface alone did not lead to radiation brightening. The results suggest that lysines situated within the more rigid structural part of the coat protein provide the chemical environments conducive to radiation brightening, and we discuss some of the characteristics of these environments.
- Published
- 2021
28. Cowpea chlorotic mottle virus‐like particles as potential platform for antisense oligonucleotide delivery in posterior segment ocular diseases
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Astrid Subrizi, Arto Urtti, Jan C. M. van Hest, Mei Chen, Miao Tang, Chiara Pretto, Heping Xu, Bio-Organic Chemistry, ICMS Core, and Institute for Complex Molecular Systems
- Subjects
Polymers and Plastics ,miR-23 ,Oligonucleotides ,Bioengineering ,02 engineering and technology ,010402 general chemistry ,virus-like particles ,01 natural sciences ,Biomaterials ,Materials Chemistry ,Gene silencing ,Cowpea chlorotic mottle virus ,Locked nucleic acid ,locked nucleic acid ,biology ,Oligonucleotide ,Chemistry ,Endothelial Cells ,Transfection ,Oligonucleotides, Antisense ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Molecular biology ,Bromovirus ,eye diseases ,0104 chemical sciences ,transfection ,Lipofectamine ,Nucleic acid ,Nanoparticles ,Nanocarriers ,antisense oligonucleotides ,0210 nano-technology ,cross-linking ,Biotechnology - Abstract
Due to its small size, easy accessibility and immune privileged environment, the eye represents an ideal target for therapeutic nucleic acids in the treatment of posterior segment ocular diseases, such as age-related macular degeneration (AMD). Among nanocarriers that can be used to achieve nucleic acid delivery, virus-like particles (VLPs) obtained from the Cowpea chlorotic mottle virus (CCMV) are an appealing platform, because of their loading capacity, ease of manufacture and amenability for functionalization. Herein, antisense oligonucleotide-loaded CCMV nanoparticles, intended for intravitreal injection, are evaluated for selective silencing of miR-23, an important target in AMD. CCMV nanoparticles loaded with anti-miR-23 locked nucleic acid and stabilized using the 3,3′-dithiobis(sulfosuccinimidyl propionate) (DTSSP) cross-linker, are assembled in vitro with a loading efficiency up to 80%. VLPs are found to be stable at 37 °C in the vitreous humor up to 24 hours. Nanoparticle cytotoxicity, cellular uptake and transfection efficacy are evaluated in endothelial cells. Selective miRNA down-regulation is achieved by the loaded CCMV VLPs both in absence and presence of Lipofectamine, with efficacies of ≈40% and more than 80%, respectively. The authors' findings pave the way for the future development of CCMV nanoparticles as oligonucleotide delivery platform to treat posterior segment ocular diseases.
- Published
- 2021
29. Efficient Purification of Cowpea Chlorotic Mottle Virus by a Novel Peptide Aptamer.
- Author
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Tscheuschner G, Ponader M, Raab C, Weider PS, Hartfiel R, Kaufmann JO, Völzke JL, Bosc-Bierne G, Prinz C, Schwaar T, Andrle P, Bäßler H, Nguyen K, Zhu Y, Mey ASJS, Mostafa A, Bald I, and Weller MG
- Subjects
- Capsid Proteins metabolism, Capsid metabolism, Bromovirus, Aptamers, Peptide analysis, Aptamers, Peptide metabolism, Nanoparticles
- Abstract
The cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses are key steps. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of the CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. Furthermore, it was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.
- Published
- 2023
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30. A conserved viral amphipathic helix governs the replication site-specific membrane association
- Author
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Preethi Sathanantham, Wenhao Zhao, Guijuan He, Austin Murray, Emma Fenech, Arturo Diaz, Maya Schuldiner, and Xiaofeng Wang
- Subjects
viruses ,Immunology ,Saccharomyces cerevisiae ,Endoplasmic Reticulum ,Virus Replication ,Bromovirus ,Microbiology ,Viral Proteins ,Infectious Diseases ,Virology ,Genetics ,Humans ,RNA, Viral ,Parasitology ,Infection ,Molecular Biology - Abstract
Positive-strand RNA viruses assemble their viral replication complexes (VRCs) on specific host organelle membranes, yet it is unclear how viral replication proteins recognize and what motifs or domains in viral replication proteins determine their localizations. We show here that an amphipathic helix, helix B in replication protein 1a of brome mosaic virus (BMV), is necessary for 1a’s localization to the nuclear endoplasmic reticulum (ER) membrane where BMV assembles its VRCs. Helix B is also sufficient to target soluble proteins to the nuclear ER membrane in yeast and plant cells. We further show that an equivalent helix in several plant- and human-infecting viruses of the alphavirus-like superfamily targets fluorescent proteins to the organelle membranes where they form their VRCs, including ER, vacuole, and Golgi membranes. Our work reveals a conserved helix that governs the localization of VRCs among a group of viruses and points to a possible target for developing broad-spectrum antiviral strategies.
- Published
- 2022
31. Fluorescent nanodiamonds encapsulated by
- Author
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Yingke, Wu, Shuqin, Cao, Md Noor A, Alam, Marco, Raabe, Sandra, Michel-Souzy, Zuyuan, Wang, Manfred, Wagner, Anna, Ermakova, Jeroen J L M, Cornelissen, and Tanja, Weil
- Subjects
Chemistry ,Biocompatible Materials ,Capsid Proteins ,Capsules ,Particle Size ,Bromovirus ,Fluorescence ,Nanodiamonds - Abstract
Long-term tracking of nanoparticles to resolve intracellular structures and motions is essential to elucidate fundamental parameters as well as transport processes within living cells. Fluorescent nanodiamond (ND) emitters provide cell compatibility and very high photostability. However, high stability, biocompatibility, and cellular uptake of these fluorescent NDs under physiological conditions are required for intracellular applications. Herein, highly stable NDs encapsulated with Cowpea chlorotic mottle virus capsid proteins (ND-CP) are prepared. A thin capsid protein layer is obtained around the NDs, which imparts reactive groups and high colloidal stability, while retaining the opto-magnetic properties of the coated NDs as well as the secondary structure of CPs adsorbed on the surface of NDs. In addition, the ND-CP shows excellent biocompatibility both in vitro and in vivo. Long-term 3D trajectories of the ND-CP with fine spatiotemporal resolutions are recorded; their intracellular motions are analyzed by different models, and the diffusion coefficients are calculated. The ND-CP with its brilliant optical properties and stability under physiological conditions provides us with a new tool to advance the understanding of cell biology, e.g., endocytosis, exocytosis, and active transport processes in living cells as well as intracellular dynamic parameters., Fluorescent nanodiamonds are stabilized by a corona of virus capsid proteins. Intracellular diffusion studies were performed suggesting that virus-coated nanodiamonds could be attractive tools for conceptual understanding of cell-virus interactions.
- Published
- 2021
32. An engineered mutant of a host phospholipid synthesis gene inhibits viral replication without compromising host fitness
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Guijuan He, Xin Zhang, Lianhui Xie, Z.J. Wu, Preethi Sathanantham, Zhenlu Zhang, and Xiaofeng Wang
- Subjects
0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Phosphatidylethanolamine N-Methyltransferase ,viruses ,Mutant ,Saccharomyces cerevisiae ,Endoplasmic Reticulum ,Virus Replication ,medicine.disease_cause ,Microbiology ,Biochemistry ,Virus ,Viral Proteins ,03 medical and health sciences ,Brome mosaic virus ,Protein targeting ,medicine ,Molecular Biology ,Gene ,Phospholipids ,030102 biochemistry & molecular biology ,biology ,Perinuclear endoplasmic reticulum ,food and beverages ,Cell Biology ,biology.organism_classification ,Bromovirus ,Cell biology ,030104 developmental biology ,Viral replication ,Viral replication complex ,Phosphatidylcholines ,RNA, Viral ,Genetic Engineering - Abstract
Viral infections universally rely on numerous hijacked host factors to be successful. It is therefore possible to control viral infections by manipulating host factors that are critical for viral replication. Given that host genes may play essential roles in certain cellular processes, any successful manipulations for virus control should cause no or mild effects on host fitness. We previously showed that a group of positive-strand RNA viruses enrich phosphatidylcholine (PC) at the sites of viral replication. Specifically, brome mosaic virus (BMV) replication protein 1a interacts with and recruits a PC synthesis enzyme, phosphatidylethanolamine methyltransferase, Cho2p, to the viral replication sites that are assembled on the perinuclear endoplasmic reticulum (ER) membrane. Deletion of the CHO2 gene inhibited BMV replication by 5-fold; however, it slowed down host cell growth as well. Here, we show that an engineered Cho2p mutant supports general PC synthesis and normal cell growth but blocks BMV replication. This mutant interacts and colocalizes with BMV 1a but prevents BMV 1a from localizing to the perinuclear ER membrane. The mislocalized BMV 1a fails to induce the formation of viral replication complexes. Our study demonstrates an effective antiviral strategy in which a host lipid synthesis gene is engineered to control viral replication without comprising host growth.
- Published
- 2019
33. RNA phloem transport mediated by pre-miRNA and viral tRNA-like structures
- Author
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Ekaterina A. Lazareva, Andrey G. Solovyev, Alexander A. Lezzhov, Anastasia K. Atabekova, and Eugeny A. Tolstyko
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant Science ,Phloem ,01 natural sciences ,03 medical and health sciences ,Cucurbita ,RNA, Transfer ,Brome mosaic virus ,Genetics ,Tobacco mosaic virus ,Phloem transport ,Tymovirus ,Turnip yellow mosaic virus ,biology ,fungi ,food and beverages ,RNA ,General Medicine ,biology.organism_classification ,Potato virus X ,Bromovirus ,Cell biology ,Potexvirus ,Tobacco Mosaic Virus ,MicroRNAs ,030104 developmental biology ,RNA, Plant ,Transfer RNA ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Phloem-mobile mRNAs are assumed to contain sequence elements directing RNA to the phloem translocation pathway. One of such elements is represented by tRNA sequences embedded in untranslated regions of many mRNAs, including those proved to be mobile. Genomic RNAs of a number of plant viruses possess a 3'-terminal tRNA-like structures (TLSs) only distantly related to genuine tRNAs, but nevertheless aminoacylated and capable of interaction with some tRNA-binding proteins. Here, we elaborated an experimental system for analysis of RNA phloem transport based on an engineered RNA of Potato virus X capable of replication, but not encapsidation and movement in plants. The TLSs of Brome mosaic virus, Tobacco mosaic virus and Turnip yellow mosaic virus were demonstrated to enable the phloem transport of foreign RNA. A miRNA precursor, pre-miR390b, was also found to render RNA competent for the phloem transport. In line with this, sequences of miRNA precursors were identified in a Cucurbita maxima phloem transcriptome, supporting the hypothesis that, at least in some cases, miRNA phloem signaling can involve miRNA precursors. Collectively, the data presented here suggest that RNA molecules can be directed into the phloem translocation pathway by structured RNA elements such as those of viral TLSs and miRNA precursors.
- Published
- 2019
34. Characterization of an Ohio Isolate of Brome Mosaic Virus and Its Impact on the Development and Yield of Soft Red Winter Wheat
- Author
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Pierce A. Paul, Jorge David Salgado, Lucy R. Stewart, and B. A. Hodge
- Subjects
biology ,viruses ,Winter wheat ,food and beverages ,Plant Science ,biology.organism_classification ,Bromovirus ,Agronomy ,Brome mosaic virus ,Yield (wine) ,Seasons ,Edible Grain ,Agronomy and Crop Science ,Triticum ,Ohio ,Field conditions - Abstract
Brome mosaic virus (BMV) is generally thought to be of little economic importance to crops; consequently, there is little information about its impact on wheat production under field conditions. After repeated detection of BMV in Ohio wheat fields at incidences up to 25%, the virus was isolated, sequenced, characterized, and tested for its impact on soft red winter wheat (SRWW). The Ohio isolate of brome mosaic virus (BMV-OH) was found to be >99% identical to a BMV-Fescue isolate (accession no. DQ530423-25) and capable of systemically infecting multiple monocot and dicot species, including cowpea and soybean, in experimental inoculations. BMV-OH was used in field experiments during the 2016 and 2017 growing seasons to quantify its effect on SRWW grain yield and development when inoculated at Feekes 1, 5, 8, and 10 in two to four cultivars. Cultivar and timing of inoculation had statistically significant (P < 0.05) main and interaction effects on grain yield, wheat growth, and multiple components of yield. Compared with noninoculated controls, BMV-OH reduced grain yield by up to 61% when inoculated at Feekes 1 and by as much as 25, 36, and 31% for inoculations at Feekes 5, 8, and 10, respectively. The magnitude of the yield reduction varied among cultivars and was associated with reductions in grain size and weight or plant population. These findings suggest that BMV could impact wheat productivity in Ohio and will serve as the basis for more large-scale investigations of the effects of this virus in commercial fields.
- Published
- 2019
35. Virus-Like Particles Produced Using the Brome Mosaic Virus Recombinant Capsid Protein Expressed in a Bacterial System
- Author
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Jakub Jagielski, Karol Kamel, Grzegorz Nowaczyk, Marek Figlerowicz, Anna Urbanowicz, Aleksander Strugała, and Marcin Radom
- Subjects
Models, Molecular ,viruses ,02 engineering and technology ,010402 general chemistry ,virus-like particles ,01 natural sciences ,complex mixtures ,Catalysis ,Virus ,Article ,law.invention ,Inorganic Chemistry ,lcsh:Chemistry ,Brome mosaic virus ,RNA, Transfer ,law ,brome mosaic virus ,Escherichia coli ,capsid ,Physical and Theoretical Chemistry ,Particle Size ,Molecular Biology ,lcsh:QH301-705.5 ,Spectroscopy ,biology ,Chemistry ,Organic Chemistry ,Temperature ,Virion ,virus diseases ,General Medicine ,self-assembly ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Bromovirus ,Polyelectrolyte ,Recombinant Proteins ,0104 chemical sciences ,Computer Science Applications ,Capsid ,lcsh:Biology (General) ,lcsh:QD1-999 ,Ionic strength ,Transfer RNA ,Biophysics ,Recombinant DNA ,Capsid Proteins ,Self-assembly ,0210 nano-technology - Abstract
Virus-like particles (VLPs), due to their nanoscale dimensions, presence of interior cavities, self-organization abilities and responsiveness to environmental changes, are of interest in the field of nanotechnology. Nevertheless, comprehensive knowledge of VLP self-assembly principles is incomplete. VLP formation is governed by two types of interactions: protein–cargo and protein–protein. These interactions can be modulated by the physicochemical properties of the surroundings. Here, we used brome mosaic virus (BMV) capsid protein produced in an E. coli expression system to study the impact of ionic strength, pH and encapsulated cargo on the assembly of VLPs and their features. We showed that empty VLP assembly strongly depends on pH whereas ionic strength of the buffer plays secondary but significant role. Comparison of VLPs containing tRNA and polystyrene sulfonic acid (PSS) revealed that the structured tRNA profoundly increases VLPs stability. We also designed and produced mutated BMV capsid proteins that formed VLPs showing altered diameters and stability compared to VLPs composed of unmodified proteins. We also observed that VLPs containing unstructured polyelectrolyte (PSS) adopt compact but not necessarily more stable structures. Thus, our methodology of VLP production allows for obtaining different VLP variants and their adjustment to the incorporated cargo.
- Published
- 2021
36. Virus Mechanics under Molecular Crowding
- Author
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Paul van deer Schoot, Cheng Zeng, Andrey G. Malyutin, Roya Zandi, Bogdan Dragnea, Liam Scott, Soft Matter and Biological Physics, and ICMS Core
- Subjects
Osmotic shock ,viruses ,Genome, Viral ,010402 general chemistry ,01 natural sciences ,Virus ,Capsid ,Brome mosaic virus ,0103 physical sciences ,Materials Chemistry ,Osmotic pressure ,Physical and Theoretical Chemistry ,High concentration ,010304 chemical physics ,biology ,Chemistry ,RNA ,biology.organism_classification ,Crowding ,Bromovirus ,0104 chemical sciences ,Surfaces, Coatings and Films ,Biophysics ,RNA, Viral ,Capsid Proteins - Abstract
Viruses avoid exposure of the viral genome to harmful agents with the help of a protective protein shell known as the capsid. A secondary effect of this protective barrier is that macromolecules that may be in high concentration on the outside cannot freely diffuse across it. Therefore, inside the cell and possibly even outside, the intact virus is generally under a state of osmotic stress. Viruses deal with this type of stress in various ways. In some cases, they might harness it for infection. However, the magnitude and influence of osmotic stress on virus physical properties remains virtually unexplored for single-stranded RNA viruses - the most abundant class of viruses. Here, we report on how a model system for the positive-sense RNA icosahedral viruses, brome mosaic virus (BMV), responds to osmotic pressure. Specifically, we study the mechanical properties and structural stability of BMV under controlled molecular crowding conditions. We show that BMV is mechanically reinforced under a small external osmotic pressure but starts to yield after a threshold pressure is reached. We explain this mechanochemical behavior as an effect of the molecular crowding on the entropy of the "breathing"fluctuation modes of the virus shell. The experimental results are consistent with the viral RNA imposing a small negative internal osmotic pressure that prestresses the capsid. Our findings add a new line of inquiry to be considered when addressing the mechanisms of viral disassembly inside the crowded environment of the cell.
- Published
- 2021
37. Controlling the surface charge of simple viruses
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Charles M. Knobler, William M. Gelbart, Jaime Ruiz-Garcia, Maria V. Villagrana-Escareño, and A. L. Duran-Meza
- Subjects
viruses ,Cell Membranes ,Virus Replication ,Biochemistry ,Viral Packaging ,Virions ,Brome mosaic virus ,Medicine and Health Sciences ,Drug Interactions ,Lipid bilayer ,Gel Electrophoresis ,Multidisciplinary ,biology ,Chemistry ,Bromovirus ,Lipids ,Capsid ,Medicine ,RNA, Viral ,Cellular Structures and Organelles ,Research Article ,Science ,Agarose Gel Electrophoresis ,Viral Structure ,Research and Analysis Methods ,Microbiology ,Electrophoretic Techniques ,Gene Delivery ,Viral envelope ,Plant virus ,Virology ,Gene Expression and Vector Techniques ,Surface charge ,Molecular Biology Techniques ,Molecular Biology ,Cowpea chlorotic mottle virus ,Pharmacology ,Molecular Biology Assays and Analysis Techniques ,Virus Assembly ,Osmolar Concentration ,Biology and Life Sciences ,Hordeum ,Cell Biology ,biology.organism_classification ,Viral Replication ,Plant Leaves ,Isoelectric point ,Biophysics ,Lipid Bilayer ,Capsid Proteins - Abstract
The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or–in the instance of virus-like particles–encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems.
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- 2021
38. Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays
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Sanjay Mehta, Soo Khim Chan, Isabel G. Newton, Pinyi Du, Caroline Ignacio, and Nicole F. Steinmetz
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Polymers and Plastics ,RNase P ,viruses ,Loop-mediated isothermal amplification ,Bioengineering ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Virus ,Biomaterials ,Materials Chemistry ,Humans ,Cowpea chlorotic mottle virus ,biology ,Chemistry ,SARS-CoV-2 ,RNA ,COVID-19 ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Virology ,Bromovirus ,Reverse transcriptase ,0104 chemical sciences ,Real-time polymerase chain reaction ,Molecular Diagnostic Techniques ,COVID-19 Nucleic Acid Testing ,0210 nano-technology ,Bacteriophage Qβ ,Nucleic Acid Amplification Techniques - Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and inexpensive isothermal alternative to the current gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, unlike RT-qPCR, there are no consensus detection regions or optimal RT-LAMP methods, and most protocols do not include internal controls to ensure reliability. Naked RNAs, plasmids, or even RNA from infectious COVID-19 patients have been used as external positive controls for RT-LAMP assays, but such reagents lack the stability required for full-process control. To overcome the lack of proper internal and external positive controls and the instability of the detection RNA, we developed virus-like particles (VLPs) using bacteriophage Qβ and plant virus cowpea chlorotic mottle virus (CCMV) for the encapsidation of target RNA, namely a so-called SARS-CoV-2 LAMP detection module (SLDM). The target RNA is a truncated segment of the SARS-CoV-2 nucleocapsid (N) gene and human RNase P gene (internal control) as positive controls for RT-qPCR and RT-LAMP. Target RNAs stably encapsidated in Qβ and CCMV VLPs were previously shown to function as full-process controls in RT-qPCR assays, and here we show that SLDMs can fulfill the same function for RT-LAMP and swab-to-test (direct RT-LAMP with heat lysis) assays. The SLDM was validated in a clinical setting, highlighting the promise of VLPs as positive controls for molecular assays.
- Published
- 2021
39. Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses.
- Author
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Ahola, Tero and Karlin, David G.
- Subjects
- *
SEQUENCE analysis , *BIOMATHEMATICS , *ENZYMES , *CATALYSTS , *ALPHAVIRUSES - Abstract
Background: Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rubella virus. They encode a capping enzyme with methyltransferase-guanylyltransferase (MTase-GTase) activity, which is an attractive drug target owing to its unique mechanism. However, its experimental study has proven very difficult. Results: We examined over 50 genera of viruses by sequence analyses. Earlier studies showed that the MTase-GTase contains a "Core" region conserved in sequence. We show that it is followed by a long extension, which we termed "Iceberg" region, whose secondary structure, but not sequence, is strikingly conserved throughout the alphavirus supergroup. Sequence analyses strongly suggest that the minimal capping domain corresponds to the Core and Iceberg regions combined, which is supported by earlier experimental data. The Iceberg region contains all known membrane association sites that contribute to the assembly of viral replication factories. We predict that it may also contain an overlooked, widely conserved membrane-binding amphipathic helix. Unexpectedly, we detected a sequence homolog of the alphavirus MTase-GTase in taxa related to nodaviruses and to chronic bee paralysis virus. The presence of a capping enzyme in nodaviruses is biologically consistent, since they have capped genomes but replicate in the cytoplasm, where no cellular capping enzyme is present. The putative MTase-GTase domain of nodaviruses also contains membrane-binding sites that may drive the assembly of viral replication factories, revealing an unsuspected parallel with the alphavirus supergroup. Conclusions: Our work will guide the functional analysis of the alphaviral MTase-GTase and the production of domains for structure determination. The identification of a homologous domain in a simple model system, nodaviruses, which replicate in numerous eukaryotic cell systems (yeast, flies, worms, mammals, and plants), can further help crack the function and structure of the enzyme. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
40. Virus-Based Nanoreactors with GALT Activity for Classic Galactosemia Therapy
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Rafael Vazquez-Duhalt, Karla Juarez-Moreno, Javier Pérez-Robles, Ruben D. Cadena-Nava, and Pedro Gama
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Galactosemias ,Drug Compounding ,Nanoreactor ,01 natural sciences ,Biochemistry ,Virus ,Cell Line ,Mice ,Drug Discovery ,medicine ,Animals ,Humans ,Nanotechnology ,UTP-Hexose-1-Phosphate Uridylyltransferase ,General Pharmacology, Toxicology and Pharmaceutics ,Fibroblast ,Pharmacology ,chemistry.chemical_classification ,010405 organic chemistry ,Organic Chemistry ,Galactosemia ,Substrate (chemistry) ,medicine.disease ,Bromovirus ,Endocytosis ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,Kinetics ,Enzyme ,medicine.anatomical_structure ,Capsid ,chemistry ,Cell culture ,Molecular Medicine ,Capsid Proteins ,Fluorescein-5-isothiocyanate - Abstract
Enzymatic nanoreactors were obtained by galactose-1-phosphate uridylyl-transferase (GALT) encapsulation into plant virus capsids by a molecular self-assembly strategy. The aim of this work was to produce virus-like nanoparticles containing GALT for an enzyme-replacement therapy for classic galactosemia. The encapsulation efficiency and the catalytic constants of bio-nanoreactors were determined by using different GALT and virus coat protein ratios. The substrate affinity of nanoreactors was slightly lower than that of the free enzyme; the activity rate was 16 % of the GALT free enzyme. The enzymatic nanoreactors without functionalization were internalized into different cell lines including fibroblast and kidney cells, but especially into hepatocytes. The enzymatic nanoreactors are an innovative enzyme preparation with potential use for the treatment of classic galactosemia.
- Published
- 2020
41. Self-Assembly of Viral Capsid Proteins Driven by Compressible Nanobubbles
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Minmin Zhang, Shuqin Cao, Jeroen J. L. M. Cornelissen, Serge G. Lemay, Aijie Liu, Bio electronics, Biomolecular Nanotechnology, and MESA+ Institute
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Cowpea chlorotic mottle virus ,Aqueous solution ,biology ,Chemistry ,viruses ,UT-Hybrid-D ,biology.organism_classification ,Microscopy, Atomic Force ,Bromovirus ,Virus ,Dynamic Light Scattering ,Nanostructures ,Colloid ,Dynamic light scattering ,Capsid ,Microscopy, Electron, Transmission ,Transmission electron microscopy ,Biophysics ,General Materials Science ,Capsid Proteins ,Self-assembly ,Physical and Theoretical Chemistry - Abstract
Colloidal nanobubbles occur in gas-saturated aqueous solutions following high power water electrolysis. Here the influence of nanobubble solutions on the self-assembly properties of viral capsid proteins (CP) was investigated. Interestingly, we found that gas solutions were able to trigger the self-assembly of CP of cowpea chlorotic mottle virus (CCMV) in the absence of the viral genome, most likely by acting as a negatively charged template. The process was demonstrated by three distinct techniques, namely, dynamic light scattering (DLS), atomic force microscopy (AFM), and transmission electron microscopy (TEM). Furthermore, nanobubble-induced self-assembly of viral CP was found to depend on protein concentration. Low CP concentrations led to assembly of 18 nm virus-like particles (VLPs), comparable to T = 1 (Casper and Klug triangulation number) virus capsids, whereas high CP concentrations led to 28 nm VLPs (similar to T = 3 capsids). This paves a new route for self-assembly of VLPs.
- Published
- 2020
42. Biomimetic Virus-Like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools
- Author
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Soo Khim Chan, Nicole F. Steinmetz, Caroline Ignacio, Isabel G. Newton, Pinyi Du, and Sanjay Mehta
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viruses ,General Physics and Astronomy ,02 engineering and technology ,01 natural sciences ,Bacteriophage ,COVID-19 Testing ,Biomimetics ,Nanotechnology ,General Materials Science ,Bacteriophages ,Viral ,Lung ,phage Qβ ,Vaccines ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,General Engineering ,021001 nanoscience & nanotechnology ,Bromovirus ,Reverse transcription polymerase chain reaction ,Infectious Diseases ,phage Q beta ,Pneumonia & Influenza ,RNA, Viral ,RNA extraction ,Infection ,0210 nano-technology ,Biotechnology ,010402 general chemistry ,virus-like particles ,Virus ,Article ,Vaccine Related ,reverse transcription polymerase chain reaction ,Biodefense ,Plant virus ,Genetics ,Humans ,Vaccines, Virus-Like Particle ,Nanoscience & Nanotechnology ,Cowpea chlorotic mottle virus ,SARS-CoV-2 ,Prevention ,RNA ,COVID-19 ,Reproducibility of Results ,Pneumonia ,biology.organism_classification ,Virology ,COVID-19, SARS-CoV-2 ,0104 chemical sciences ,Virus-Like Particle ,Kinetics ,Emerging Infectious Diseases ,Nucleic acid ,cowpea chlorotic mottle virus - Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible disease that has affected more than 90% of the countries worldwide. At least 17 million individuals have been infected, and some countries are still battling first or second waves of the pandemic. Nucleic acid tests, especially reverse transcription polymerase chain reaction (RT-PCR), have become the workhorse for early detection of COVID-19 infection. Positive controls for the molecular assays have been developed to validate each test and to provide high accuracy. However, most available positive controls require cold-chain distribution and cannot serve as full-process control. To overcome these shortcomings, we report the production of biomimetic virus-like particles (VLPs) as SARS-CoV-2 positive controls. A SARS-CoV-2 detection module for RT-PCR was encapsidated into VLPs from a bacteriophage and a plant virus. The chimeric VLPs were obtained either by in vivo reconstitution and coexpression of the target detection module and coat proteins or by in vitro assembly of purified detection module RNA sequences and coat proteins. These VLP-based positive controls mimic SARS-CoV-2 packaged ribonucleic acid (RNA) while being noninfectious. Most importantly, we demonstrated that the positive controls are scalable, stable, and can serve broadly as controls, from RNA extraction to PCR in clinical settings.
- Published
- 2020
43. The impact of size on particle drainage dynamics and antibody response
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Simon, Zinkhan, Anete, Ogrina, Ina, Balke, Gunta, Reseviča, Andris, Zeltins, Simone, de Brot, Cyrill, Lipp, Xinyue, Chang, Lisha, Zha, Monique, Vogel, Martin F, Bachmann, and Mona O, Mohsen
- Subjects
Epitopes ,Antibody Formation ,Escherichia coli ,Drainage ,Vaccines, Virus-Like Particle ,Bromovirus - Abstract
Vaccine-induced immune response can be greatly enhanced by mimicking pathogen properties. The size and the repetitive geometric shape of virus-like particles (VLPs) influence their immunogenicity by facilitating drainage to secondary lymphoid organs and enhancing interaction with and activation of B cells and innate humoral immune components. VLPs derived from the plant Bromovirus genus, specifically cowpea chlorotic mottle virus (CCMV), are T = 3 icosahedral particles. (T) is the triangulation number that refers to the number and arrangements of the subunits (pentamers and hexamers) of the VLPs. CCMV-VLPs can be easily expressed in an E. coli host system and package ssRNA during the expression process. Recently, we have engineered CCMV-VLPs by incorporating the universal tetanus toxin (TT) epitope at the N-terminus. The modified CCMV
- Published
- 2020
44. Virus Assembly Pathways: Straying Away but Not Too Far
- Author
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Martin F. Jarrold, Bogdan Dragnea, Irina B. Tsvetkova, Joseph Che Yen Wang, and Kevin M. Bond
- Subjects
viruses ,Cell ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Genome ,Virus ,Biomaterials ,Capsid ,Brome mosaic virus ,medicine ,General Materials Science ,biology ,Chemistry ,Virus Assembly ,Cryoelectron Microscopy ,Virion ,food and beverages ,RNA ,General Chemistry ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Bromovirus ,In vitro ,0104 chemical sciences ,Cell biology ,medicine.anatomical_structure ,Nucleic acid ,RNA, Viral ,Capsid Proteins ,0210 nano-technology ,Biotechnology - 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.
- Published
- 2020
45. Genome organization and interaction with capsid protein in a multipartite RNA virus
- Author
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William M. Gelbart, Charles M. Knobler, A. L. N. Rao, Z. Hong Zhou, Xue Yang, Yanxiang Cui, Antara Chakravarty, and Christian Beren
- Subjects
viruses ,cryoelectron microscopy ,Genome, Viral ,virus ,Biology ,Brome mosaic virus ,Sense (molecular biology) ,Genetics ,Bacteriophages ,Viral ,Single-Stranded RNA ,Multidisciplinary ,Genome ,RNA Conformation ,food and beverages ,RNA ,RNA virus ,biology.organism_classification ,Bromovirus ,Multipartite ,Capsid ,single-stranded RNA ,Physical Sciences ,RNA, Viral ,Capsid Proteins ,Infection - Abstract
We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content—specifically, RNAs 3 and 4—assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific “packaging signals” throughout the viral RNA to package their monopartite genomes.
- Published
- 2020
46. Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo
- Author
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Antara Chakravarthy, Vijay S. Reddy, and A. L. N. Rao
- Subjects
viruses ,Immunology ,Agrobacterium ,Genome, Viral ,Virus Replication ,Peptide Mapping ,Microbiology ,Capsid ,Viral life cycle ,Brome mosaic virus ,Virology ,medicine ,Gene ,Subgenomic mRNA ,biology ,Virus Assembly ,Structure and Assembly ,Virion ,RNA ,RNA virus ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Trypsin ,Bromovirus ,RNA, Bacterial ,Insect Science ,Biophysics ,RNA, Viral ,Capsid Proteins ,medicine.drug - Abstract
Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1(V)) and type 2 (B2(V)) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4(V)) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta. Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K(65), R(103), K(111), and K(165) on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1(V) and B2(V) released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4(V) capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids. IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
- Published
- 2020
47. How a Virus Circumvents Energy Barriers to Form Symmetric Shells
- Author
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Rafael Leite Rubim, Sanaz Panahandeh, Laurent Marichal, Roya Zandi, Siyu Li, Guillaume Tresset, Laboratoire de Physique des Solides (LPS), and Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Surface Properties ,Icosahedral symmetry ,nucleation ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,Nucleation ,Shell (structure) ,FOS: Physical sciences ,General Physics and Astronomy ,02 engineering and technology ,Molecular Dynamics Simulation ,Condensed Matter - Soft Condensed Matter ,010402 general chemistry ,01 natural sciences ,elastic energy ,law.invention ,law ,kinetic pathways ,General Materials Science ,Physics - Biological Physics ,Particle Size ,Chemistry ,Cryoelectron Microscopy ,General Engineering ,Elastic energy ,Biomolecules (q-bio.BM) ,021001 nanoscience & nanotechnology ,Bromovirus ,0104 chemical sciences ,Nucleoprotein ,Quantitative Biology - Biomolecules ,Capsid ,viral shells ,Biological Physics (physics.bio-ph) ,Chemical physics ,FOS: Biological sciences ,DNA, Viral ,RNA, Viral ,Soft Condensed Matter (cond-mat.soft) ,Capsid Proteins ,Self-assembly ,Electron microscope ,0210 nano-technology ,Monte Carlo Method ,Metrics & More Article Recommendations self-assembly - Abstract
Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly ordered structure in the host cell. Using small-angle X-ray scattering, we find out that a disorder-order transition occurs under physiological conditions upon an increase in capsid protein concentrations. Our cryo-transmission electron microscopy reveals closed spherical shells containing in vitro transcribed viral RNA even at pH 7.5, in marked contrast with the previous observations. We use Monte Carlo simulations to explain this disorder-order transition and find that, as the shell grows, the structures of disordered intermediates in which the distribution of pentamers does not belong to the icosahedral subgroups become energetically so unfavorable that the caps can easily dissociate and reassemble overcoming the energy barriers for the formation of perfect icosahedral shells. In addition, we monitor the growth of capsids under the condition that the nucleation and growth is the dominant pathway and show that the key for the disorder-order transition in both en masse and nucleation and growth pathways lies in the strength of elastic energy compared to the other forces in the system including protein-protein interactions and the chemical potential of free subunits. Our findings explain, at least in part, why perfect virions with icosahedral order form under different conditions including physiological ones., Comment: 17 pages, 21 figures, 1 table, 1 appendix
- Published
- 2020
48. A conserved viral amphipathic helix governs the replication site-specific membrane association.
- Author
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Sathanantham P, Zhao W, He G, Murray A, Fenech E, Diaz A, Schuldiner M, and Wang X
- Subjects
- Endoplasmic Reticulum metabolism, Humans, Saccharomyces cerevisiae genetics, Viral Proteins metabolism, Virus Replication, Bromovirus, RNA, Viral metabolism
- Abstract
Positive-strand RNA viruses assemble their viral replication complexes (VRCs) on specific host organelle membranes, yet it is unclear how viral replication proteins recognize and what motifs or domains in viral replication proteins determine their destinations. We show here that an amphipathic helix, helix B in replication protein 1a of brome mosaic virus (BMV), is necessary for 1a's localization to the nuclear endoplasmic reticulum (ER) membrane where BMV assembles its VRCs. Helix B is also sufficient to target soluble proteins to the nuclear ER membrane in yeast and plant cells. We further show that an equivalent helix in several plant- and human-infecting viruses of the Alsuviricetes class targets fluorescent proteins to the organelle membranes where they form their VRCs, including ER, vacuole, and Golgi membranes. Our work reveals a conserved helix that governs the localization of VRCs among a group of viruses and points to a possible target for developing broad-spectrum antiviral strategies., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
- Full Text
- View/download PDF
49. Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.
- Author
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Szoverfi J and Fejer SN
- Subjects
- Capsid chemistry, Capsid Proteins metabolism, Molecular Dynamics Simulation, Sodium Chloride metabolism, Bromovirus
- Abstract
Intermediates of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales either by studying oligomers in equilibrium or by focusing on their dissociation instead of their association. Our previous studies showed that among the three possible dimer interfaces in the icosahedral capsid, two are thermodynamically relevant for capsid formation. The aim of the current study is to evaluate the relative structural stabilities of the three different ss-CCMV dimers and to find and understand the conditions that lead to their dissociation. Long timescale molecular dynamics simulations at 300 K of the various dimers and of the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. Simulations in implicit solvent show that at higher temperature (350 K), the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable interface. The pentamer of dimers is also found to be stable on long timescales at 300 K, with an inherent flexibility of the outer protein chains., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
50. Versatile Reversible Cross-Linking Strategy to Stabilize CCMV Virus Like Particles for Efficient
- Author
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Chiara, Pretto and Jan C M, van Hest
- Subjects
Cross-Linking Reagents ,Drug Delivery Systems ,Virion ,Succinimides ,RNA, Small Interfering ,Bromovirus ,Article - Abstract
Virus like particles obtained from the Cowpea Chlorotic Mottle Virus (CCMV) represent an innovative platform for drug delivery applications. Their unique reversible self-assembly properties as well as their suitability for both cargo loading and functionalization make them a versatile scaffold for numerous purposes. One of the main drawbacks of this platform is however its limited stability at physiological conditions. Herein, we report the development of a general reversible cross-linking strategy involving the homobifunctional cross-linker DTSSP (3,3′-dithiobis (sulfosuccinimidylpropionate)) which is suitable for particle stabilization. This methodology is adaptable to different CCMV variants in the presence or absence of a stabilizing cargo without varying neither particle shape nor size thus extending the potential use of these protein cages in nanomedical applications. Cross-linked particles are stable at neutral pH and 37 °C and they are capable of protecting loaded cargo against enzymatic digestion. Furthermore, the reversible nature of the cross-linking ensures particle disassembly when they are taken up by cells. This was demonstrated via the highly effective delivery of active siRNA into cells.
- Published
- 2019
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